History of Christian thought on persecution and tolerance

Development of Christian thought in the West

The history of Christian thought has included concepts of both inclusivity and exclusivity from its beginnings, that have been understood and applied differently in different ages, and have led to practices of both persecution and toleration. Early Christian thought established Christian identity, defined heresy, separated itself from polytheism and Judaism and developed the theological conviction called supersessionism. In the centuries after Christianity became the official religion of Rome, some scholars say Christianity became a persecuting religion. Others say the change to Christian leadership did not cause a persecution of pagans, and that what little violence occurred was primarily directed at non orthodox Christians. After the fall of the Roman Empire, Christian thought focused more on preservation than origination. This era of thought is exemplified by Gregory the Great, Saint Benedict, Visigothic Spain, illustrated manuscripts, and progress in medical care through monks. Although the roots of supersessionism and deicide can be traced to some second century Christian thought, Jews of the Middle Ages lived mostly peacefully alongside their Christian neighbors because of Augustine of Hippo's teaching that they should be left alone. In the Early Middle Ages, Christian thought on the military and involvement in war shifted to accommodate the crusades by inventing chivalry and new monastic orders dedicated to it. There was no single thread of Christian thought throughout most of the Middle Ages as the church was largely democratic and each order had its own doctrine. The High Middle Ages were pivotal in both European culture and Christian thought. Feudal kings began to lay the foundation of what would become their modern nations by centralizing power. They gained power through multiple means including persecution. Christian thought played a supportive role, as did the literati, a group of ambitious intellectuals who had contempt for those they thought beneath them, by verbally legitimizing those attitudes and actions. During the Northern Crusades, Christian thought on conversion shifted to a pragmatic acceptance of conversion obtained through political pressure or military coercion even though theologians of the period continued to write that conversion must be voluntary. By the time of the early Reformation (1400–1600), the conviction developed among the early Protestants that pioneering the concepts of religious freedom and religious toleration was necessary. Scholars say tolerance has never been an attitude broadly espoused by an entire society, not even western societies, and that only a few outstanding individuals, historically, have truly fought for it. In the West, Christian reformation figures, and later Enlightenment intellectuals, advocated for tolerance in the century preceding, during, and after the Reformation and into the Enlightenment. Contemporary Christians generally agree that tolerance is preferable to conflict, and that heresy and dissent are not deserving of punishment. Despite that, the systematized government supported persecution of minorities invented in the West in the High Middle Ages for garnering power to the state has spread throughout the world. Sociology indicates tolerance and persecution are products of context and group identity more than ideology.

In its first three centuries, Christian thought was just beginning to define what it meant to be a Christian, distinct from paganism and Judaism, through its definitions of orthodoxy and heterodoxy. Like the other Abrahamic religions, Christian thought has included, from its beginnings, two ideals which have affected Christian responses to alterity: inclusivity (also called universality) and exclusivity, or as David Nirenberg describes them, our "mutual capacities for coexistence and violence." Justo L. González traces three veins of Christian thought that began in the second century. Out of Carthage, Tertullian the lawyer (155–200 CE) wrote of Christianity as revelation of the law of God. From the pluralistic city of Alexandria, Origen wrote of the commonalities between philosophy and theology, reason and revelation, seeing Christianity as the intellectual pursuit of transcendent truth. In Asia Minor and Syria, Irenaeus saw Christianity as God working in human history through its pastoral work of reaching people with God's love. Each vein of thought has continued throughout Christian history, and have impacted attitudes toward and practices of tolerance and persecution.

Early Christian communities were highly inclusive in terms of social stratification and other social categories, much more so than were the Roman voluntary associations. Heterogeneity characterized the groups formed by Paul the Apostle, and the role of women was much greater than in either of the forms of Judaism or paganism in existence at the time. Tertullian, a second century Christian intellectual and lawyer from Carthage, advocated for religious tolerance primarily in an effort to convince pagan readers that Christianity should be allowed into the religious "market place" that historian John North proposes second century Rome had become. Historian Geoffrey S. Smith argues that Justin writes only to answer objections his friends are facing and to defend these friends from ill treatment and even death. He quotes Justin in a letter to the emperor as saying he is writing: "On behalf of those from every race of men who are unjustly hated and ill treated, being one of them myself."

Supersessionist thought is defined by "two core beliefs: (1) that the nation of Israel has forfeited its status as the people of God through disobedience; and (2) the New Testament church has therefore become the true Israel and inheritor of the promises made to the nation of Israel." It has three forms: punitive, economic, and/or structural supersessionism. The church took its universally held traditional interpretation of Revelation 20:4 6 (Millennialism) and its hope of the thousand year reign of the Messiah on earth, centered in Jerusalem, ruling with the redeemed Israel, says supersessionism was still considered a "normative view" in the writings of the early church fathers, such as Justin, Barnabas and Origen, and has also been a part of Christian thought for much of the church's history. John Gager makes a distinction between nineteenth century anti Semitism and second century anti Judaism, and many scholars agree, yet there are those who see early anti Judaism and later anti Semitism as the same. sv sees the development of anti semitism as part of the paradigm shift that occurred in early modernity. Gerdmar argues the shift resulted from the new scientific focus on the Bible and history that replaced the primacy of theology and tradition. Christopher Leighton associates anti Judaism with the origins of Christianity, and anti semitism with "modern nationalism and racial theories". Melito's writings were not influential, and the idea was not immediately influential, but the accusation returned in fourth century thinking and sixth century actions and again in the Middle Ages. He outlawed the gladiatorial shows, destroyed temples and plundered more, and used forceful rhetoric against non Christians. But he never engaged in a purge. "He did not punish pagans for being pagans, or Jews for being Jews, and did not adopt a policy of forced conversion." While not making a direct personal contribution to Christian thought, the first Christian Roman emperor had a powerful impact on it through the example of his own conversion, his policies, and the various councils he called. Christian thought at the time of Constantine believed that victory over the "false gods" had begun with Jesus and ended with the conversion of Constantine as the final fulfillment of heavenly victory—even though Christians were only about fifteen to eighteen percent of the empire's population. After Constantine, Christianity gradually became the dominant religion in the Roman Empire. In the view of many historians, the Constantinian shift turned Christianity from a persecuted religion into a persecuting religion. However, the claim that there was a Constantinian shift has been disputed. Theologian Peter Leithart argues that there was a "brief, ambiguous 'Constantinian moment' in the early fourth century", but that there was "no permanent, epochal 'Constantinian shift. According to Michele R. Salzman, fourth century Rome featured sociological, political, economic and religious competition, producing tensions and hostilities between various groups, but that Christians focused on heresy more than pagans.

Historians and theologians refer to the fourth century as the "golden age" of Christian thought. Figures such as John Chrysostom, Ambrose, Jerome, Basil, Gregory of Nazianus, Gregory of Nyssa, and the prolific Augustine, all made a permanent mark on Christian thought and history. They were primarily defenders of orthodoxy. They wrote philosophy and theology as well as apologetics and polemics. Some had a long term effect on tolerance and persecution in Christian thought.

Fourth century Christian thought was dominated by its many conflicts defining orthodoxy versus heterodoxy and heresy. In what remained of the Eastern Roman empire, known as Byzantium, the Arian controversy began with its debate of Trinitarian formulas which lasted 56 years. It gradually trickled over into the Latin West so that by the fourth century, the center of the controversy was the "champion of orthodoxy", Athanasius. Arianism was the reason for calling the Council of Nicea. Athanasius was ousted from his bishopric in Alexandria in 336 by the Arians, forced into exile, and lived much of the remainder of his life in a cycle of forced movement. The controversy became political after Constantine's death. Athanasius died in 373, while an Arian emperor ruled, but his orthodox teaching was a major influence in the West, and on Theodosius, who became emperor in 381. However, Chrysostom did not advocate for killing heretics, even though he did advocate censoring them; he writes, "He [Christ] doth not therefore forbid our checking heretics, and stopping their mouths, and taking away their freedom of speech, and breaking up their assemblies and confederacies, but our killing and slaying them". By 305, after the Diocletian persecution of the third century, many of those who had recanted during the persecution, wanted to return to the church. The North African Donatists refused to accept them back as clergy and remained resentful toward the Roman government. Catholics wanted to wipe the slate clean and accommodate the new government. The Donatists withdrew and began setting up their own churches. For decades, Donatists fomented protests and street violence, refused compromise, attacked random Catholics without warning, doing serious and unprovoked bodily harm such as beating people with clubs, cutting off their hands and feet, and gouging out eyes. All attempts failed. The empire responded to civil unrest with force, and in 408 in his Letter 93, Augustine began defending persecution of the Donatists by the imperial authorities saying that, "if the kings of this world could legislate against pagans and poisoners, they could do so against heretics as well." but he supported the power of the state to use coercion against those he saw as behaving as enemies. Augustine had advocated fines, imprisonment, banishment, and moderate floggings; when the state's persecution of individual Donatists became extreme, he attempted to mitigate the punishments, and he always opposed the execution of heretics. According to Henry Chadwick, Augustine "would have been horrified by the burning of heretics."

Polytheism began declining by the second century, long before there were Christian emperors, but after Constantine made Christianity officially accepted, it declined even more rapidly, and there are two views on why. According to the Oxford Handbook of Late Antiquity, scholars of Antiquity fall into two categories, holding either the "catastrophic" view, or the "long and slow" view of polytheism's decline and end. The traditional "catastrophic" view has been the established view for 200 years; it says polytheism declined rapidly in the fourth century, with a violent death in the fifth, as a result of determined anti pagan opposition from Christians, particularly Christian emperors. Laws such as the Theodosian decrees attest to Christian thought of the period, giving a "dramatic view of radical Christian ambition". Authorities, who were still mostly pagan, were lax in imposing them, and Christian bishops frequently obstructed their application. Lavan says Christian writers gave the narrative of victory high visibility, but that it does not necessarily correlate to actual conversion rates. There are many signs that a healthy paganism continued into the fifth century, and in some places, into the sixth and beyond. The Germanic tribes which had overthrown Rome became the new rulers, dividing the empire between them. Gregory the Great became Pope in 590AD, and he sent out multiple missionaries who peacefully converted Britain, Ireland, Scotland and more. Learning was kept alive in the monasteries they built which became the sole source of education for the next few centuries. In most of history, victors of war imposed their religion on the newly subjugated people, however, the Germanic tribes gradually adopted Christianity, the religion of defeated Rome, instead. This brought, in its wake, a broad process of cultural change that lasted for the next 500 years. What had been formed by the unity of the classical world and Christianity, was now transplanted into Germanic tribal culture, thereby forming a new synthesis that became western European Christendom. The church had immense influence during this time due to the endless commitment and work of the clergy and the "powerful effect of the Christian belief system" amongst the people. Scattered violence toward Jews occasionally took place during riots led by mobs, local leaders, and lower level clergy without the support of church leaders or Christian thought. Jeremy Cohen says historians generally agree this is because Catholic thought on the Jews before the 1200s was guided by the teachings of Augustine. Augustine's position on the Jews, with its accompanying argument for their "immunity from religious coercion enjoyed by virtually no other community in post Theodosian antiquity" was preceded by a positive evaluation of the Jewish past, and its relationship to divine justice and human free will. Augustine rejected those who argued that the Jews should be killed, or forcibly converted, by saying that Jews should be allowed to live in Christian societies and practice Judaism without interference because they preserved the teachings of the Old Testament and were living witnesses of the truths of the New Testament. Gregory the Great is generally seen as an important Pope in relation to the Jews. He denigrated Judaism but followed Roman Law and Augustinian thought with regard to how the Jews should be treated. He wrote against forced baptism. Even Pope Innocent III, who generally found the behavior of Jews in Christian society to be "intolerable", still agreed that the Jews should not be killed or forcibly converted when he called for the Second Crusade.

St. Benedict (480–547) was another major figure who impacted pre modern ideals of tolerance in Christian thought. Considered the father of western monasticism, he wrote his Rule around three values: community, prayer, and hospitality. This hospitality was extended to anyone without discrimination. "Pilgrims and visitors from every rank of society from crowned heads to poorest peasants, came in search of prayers or alms, protection and hospitality."

Visigothic leaders in Spain subjected the Jews to persecution and efforts to convert them forcibly for a century after 613.

Christian thought from its early days had generally frowned upon participation in the military, but that became increasingly difficult to maintain in the Middle Ages. Chivalry, a new ideal of the religious warrior who fought for justice, defended truth, and protected the weak and the innocent formed. Such a knight was ordained only after proving his spiritual and martial worth: robed in white, he would swear an oath before a cleric to uphold these values and defend the faith. Charlemagne had become King of the Franks in 771, and ruled most of western Europe of the time. He advocated Christian principles, including education, openly supported Christian missions, and had at least one Christian advisor. But he also spent his entire life fighting to defend his empire and his faith. The Franks had been fighting the Saxons since the time of Charlemagne's grandfather. Charlemagne himself began to fight the Saxons in earnest in 772, defeating them and taking hostages in a battle on the upper Weser. "Time and again the Saxon chiefs, worn down by war, sued for peace, offered hostages, accepted baptism and agreed to allow missionaries to go about their work without hindrance. But vigilance slackened, Charles was engaged on some other front, rebellions broke out, Frankish garrisons were attacked and massacred, and monasteries were pillaged". Repeatedly, Saxons rose, pillaged and looted and killed, were defeated, and rose again, until after 779, Charlemagne felt he had pacified the region and gained genuine oaths of loyalty from the Saxon leaders. After this, Charlemagne transported ten thousand families from the most turbulent district into the heart of his own territory, and the Saxons were finally settled.

From the beginning, the crusades have been seen from different points of view. Darius von Güttner Sporzyński explains that scholars continue to debate crusading and its impact so scholarship in this field is continually undergoing revision and reconsideration. Many early crusade scholars saw crusade histories as simple recitations of how events actually transpired, but by the eighteenth and nineteenth centuries, scholarship was increasingly critical and skeptical of that perspective. Simon John writes that Christopher Tyerman is in the forefront of contemporary scholarship when he says that the "earliest of crusade histories can not be regarded by scholars even in part as 'mere recitation of events.' Instead, they should be treated in their entirety as 'essays in interpretation'." At the time of the First Crusade, there was no clear concept in Christian thought of what a crusade was beyond that of a pilgrimage. says the crusades are representative of the "powerful sense in Christian thought of the time of the importance of the concreteness of Jesus' human existence The city [of Jerusalem's] importance is reflected in the fact that early medieval maps place [Jerusalem] at the center of the world." By 1935, Carl Erdmann published Die Entstehung des Kreuzzugsgedankens (The Origin of the Idea of Crusade), stressing that the crusades were essentially defensive acts on behalf of fellow Christians and pilgrims in the East who were being attacked, killed, enslaved or forcibly converted. Constable adds that those "scholars who see the crusades as the beginning of European colonialism and expansionism would have surprised people at the time. [Crusaders] would not have denied some selfish aspects but the predominant emphasis was on the defense and recovery of lands that had once been Christian and on the self sacrifice rather than the self seeking of the participants." Giles Constable says this view is common among the populace. concepts of tolerance and intolerance were not starting points for thoughts about relations for any of the various groups involved in or affected by the crusades. Instead, concepts of tolerance began to grow during the crusades from efforts to define legal limits and the nature of co existence. Ideas such as Holy War and Christian chivalry, in both Christian thought and culture, continued to evolve gradually from the eleventh to the thirteenth centuries. "The greatest of all crusader historians, William, archbishop of Tyre wrote his Chronicon from the point of view of a Latin Christian born and living in the East". and Peter D. Diehl "the growth of secular power and the pursuit of secular interests, constituted the essential context of the developments that led to a persecuting society." By the 1200s, both civil and canon law had become a major aspect of ecclesiastical culture, dominating Christian thought. Three of those new orders would have a separate but distinct impact on Christian thought on tolerance and persecution: the Dominicans, the Franciscans, and the Augustinians. Dominican thought reached beyond a simple anti heretical discourse into a broader and deeper ideology of sin, evil, justice, and punishment. They conceived themselves as fighting for truth against heterodoxy and heresy. However, in his Summa Theologica II II qu. 11, art. 3, he adds that heretics—after two fruitless admonitions—deserve only excommunication and death. The Christian thought of St. Francis was pastoral. He is recognized for his commitment to issues of social justice and his embrace of the natural world but, during his lifetime, he was also a strong advocate of conversion of the Muslims, though he believed he would likely die for it. Francis was motivated by an intense devotion to the humanity of Christ, a regard for his sufferings, and by identifying the sufferings of ordinary people with the sufferings of Christ. Through the teachings of the Franciscans, this thinking emerged from the cloister, reoriented much Christian thought toward love and compassion, and became a central theme for the ordinary Christian. there is agreement that the Order of the Hermits of St. Augustine supported the development of church hierarchy and embraced concepts such as the primacy of the Pope and his perfection. The question of church authority in the West had remained unsettled until the eleventh century when the church hierarchy worked to centralize power into the Pope. Although centralization of power was never fully achieved within the church, the era of "papal monarchy" began, and the church gradually began to resemble its secular counterparts in its conduct, thought, and objectives. Leaders reasoned that both lay and church authority had an obligation to step in when sedition, peace, or the general stability of society was part of the issue. In the Late Roman Empire, an inquisitorial system of justice had developed, and that system was revived in the Middle Ages using a combined panel (a tribunal) of both civil and ecclesiastical representatives with a bishop, his representative, or sometimes a local judge, as inquisitor. Essentially, the church reintroduced Roman law in Europe in the form of the Inquisition when it seemed that Germanic law had failed. The revival of Roman law made it possible for Pope Innocent III (1198–1216) to make heresy a political question when he took Roman law's doctrine of lèse majesté, and combined it with his view of heresy as laid out in the 1199 decretal Vergentis in senium, thereby equating heresy with treason against God.

The process of centralizing power included the development of a new kind of persecution aimed at minorities. The Fourth Lateran council reduced those penalties, and though Gregory IX (1145–1241) ordered the Dominicans to root out homosexuality from the territory that later became the nation of Germany, a century earlier, the kingdom of Jerusalem had spread a legal code ordaining death for "sodomites". From the 1250s onwards, a series of similar legal codes in the nation states of Spain, France, Italy and Germany followed this example. "By 1300, places where male sodomy was not a capitol offense had become the exception rather than the rule." In France, the constabulary was regularized in 1337 as a military body used to enforce the new laws. There were new funds to pay them as cities introduced several direct taxes: head taxes for the poor, and net worth taxes or, occasionally, crude income taxes for the rich. New gold coins, trade and the new banks also made private policing possible. The inquisitions were a new legal method that allowed the judge to investigate on his own initiative without requiring a victim (other than the state) to press charges. Together, these enabled secular leaders to gain power by making others powerless. During the fourteenth century, the kings in France and England were successful at centralizing power in their nations, and many other countries wanted to imitate them and their governing style. As part of that process, popes in this century reorganized the financial system of the church. The poor had previously been allowed to offer their tithes 'in kind', in goods and services instead of cash, but these popes revamped the system to only accept money. Bernard of Clairvaux (1090–1153), pillar of European monasticism and powerful twelfth century preacher, provides a perfect example of a Christian thinker who was balancing on a precipice, preaching hateful images of Jews but sounding Scripture based admonitions that they must be protected despite their nature." One result of the trial was that the people of Europe thought that, even if they had once had an obligation to preserve the Jews for the sake of the Old Testament, Talmudic Judaism was so different from its biblical sources that the old obligations no longer applied. In the words of Hebrew University historian Ben Zion Dinur, from 1244 on the state and the church would "consider the Jews to be a people with no religion (benei bli dat) who have no place in the Christian world."

The situation of the Jews differed from that of other victims of persecution because of their relationship with civic authorities and money. They often filled the role of financial agent or manager for the lords; they and their possessions were considered the property of the king in England; and they were often exempted from taxes and other laws because of the importance of their usury. This attracted unpopularity, jealousy and resentment from non Jews. Opposition to the barons in England led to the Jewish expulsion in 1290. The expulsion from France in 1315 coincided with the formation of the league against arbitrary royal government. In the early fourteenth century, systematic popular and judicial attack left the European Jewish community impoverished by the next century. Other scholars such as John Gager make a clear distinction between anti Judaism and anti semitism. Craig Evans defines anti Judaism as opposition to Judaism as a religion, while anti semitism is opposition to the Jewish people themselves. sv sees the development of anti semitism as part of the paradigm shift of early modernity that replaced the primacy of theology, and the tradition of Augustine, with the primacy of human reason. Aquinas does appear to believe the Jews had been cast into spiritual exile for their rejection of Christ, but he also says Jewish observance of Law continues to have positive theological significance. By 1255, when Jews were charged with Hugh of Lincoln's ritual murder, it was not the first time they had been charged with such a crime. speaks of three groups involved in the persecution of heresy: the civil authorities, the church and the people. Russell adds that heresy became common only after the Third Lateran Council in 1179. This shifted attitudes concerning the church's appropriate response. The Council of Montpellier in 1062, and the Council of Toulouse in 1119, both demanded that heretics be handed over to secular powers for coercive punishment. As most bishops thought this would be participation in shedding blood, the church refused until 1148 when the notorious and violent Eon de l'Etoile was so delivered. Eon was found mad, but a number of his followers were burned. From 1125 to 1229, Cistercian monks left their isolation and served as itinerant preachers traversing town and country in anti heretical campaigns aimed increasingly against the Albigensians. In 1209, after decades of having called upon secular rulers for aid in dealing with the Cathars and getting no response, Scholars disagree, using two distinct lines of reasoning, on whether the brutal nature of the war that followed was determined more by the Pope or by King Philip and his proxies. J. Sumption and Stephen O'Shea paint Innocent III as "the mastermind of the crusade". Markale suggests the true architect of the campaign was the French king Philip Augustus, stating that "it was Phillip who actually petitioned Innocent for permission to conduct the Crusade." Konrad Repgen writes: "The Albigensian war was indisputably a case of the interlinking of religion and politics." Some twenty years later, a story that historian Laurence W. Marvin calls apocryphal, arose about this event claiming the papal legate, Arnaud Amaury, the leader of the crusaders, was said to have responded: "Kill them all, let God sort them out." Marvin says it is unlikely the legate ever said any thing at all. "The speed and spontaneity of the attack indicates that the legate probably did not know what was going on until it was over." Marvin adds they did not kill them all at any rate: "clearly most of Bezier's population and buildings survived" and the city "continued to function as a major population center" after the campaign. Religious toleration was not considered a virtue by the people or the church of the High Middle Ages. The Pope's response was not prompt, but four years after the massacre at Béziers, in a 1213 letter to Amaury, the pope rebuked the legate for his "greedy" conduct in the war. He also canceled crusade indulgences for Languedoc, and called for an end to the campaign.

"People living during what a modern historian has termed the 'calamitous' fourteenth century were thrown into confusion and despair". George Garnett says the implementation of the papal monarchial idea had led to the loss of prestige, as the more efficient the papal bureaucratic machine became, the further it alienated the people, and the further it declined. Jan Hus (1369–1415) accepted some of Wycliff's views and aligned with the Bohemian Reform movement which was also rooted in popular piety and owed much to the evangelical preachers of fourteenth century Prague. In 1415, Hus was called to the Council of Constance where his ideas were condemned as heretical and he was handed over to the state and burned at the stake. The Fraticelli, who were also known as the "Little Brethren" or "Spiritual Franciscans", were dedicated followers of Saint Francis of Assisi. These Franciscans honored their vow of poverty and saw the wealth of the church as a contributor to corruption and injustice when so many lived in poverty. They criticized the worldly behavior of many churchmen. Thus, the Brethren were declared heretical by John XXII (1316–1334) who was called "the banker of Avignon". The leader of the brethren, Bernard Délicieux (c. 1260–1270 1320) was well known as he had spent much of his life battling the Dominican run inquisitions. After torture and threat of excommunication, he confessed to the charge of interfering with the inquisition, and was defrocked and sentenced to life in prison, in chains, in solitary confinement, and to receive nothing but bread and water. The judges attempted to ameliorate the harshness of this sentence due to his age and frailty, but Pope John XXII countermanded them and delivered the friar to Inquisitor Jean de Beaune. Délicieux died shortly thereafter in early 1320.

Conditional toleration that included discrimination was common everywhere in Europe of the Late Middle Ages and the Renaissance era. Prior to the Thirty Years' War, there was conditional toleration between Catholics and Protestants. While Frankfurt's Jews flourished between 1453 and 1613, their success came despite significant discrimination. They were restricted to one street, had rules concerning when they could leave it, and had to wear a yellow ring as a sign of their identity while outside. But within their community they also had some self governance, their own laws, elected their own leaders, and had a Rabbinical school that became a religious and cultural center. "Officially, the medieval Catholic church never advocated the expulsion of all the Jews from Christendom, or repudiated Augustine's doctrine of Jewish witness Still, late medieval Christendom frequently ignored its mandates "

Political authorities of the day maintained order by keeping groups separated both legally and physically in what would be referred to in contemporary society as segregation. By the Late Middle Ages: "The maintenance of civil order through legislated separation and discrimination was part of the institutional structure of all European states ingrained in law, politics, and the economy." but in 1543 he published On the Jews and their Lies, a "violent anti semitic tract". John Calvin helped to secure the execution for heresy of Michael Servetus, although he unsuccessfully requested that he should be beheaded instead of being burned at the stake. In England, John Foxe, John Hales, Richard Perrinchief, Herbert Thorndike and Jonas Proast all only saw mild forms of persecution against the English Dissenters as legitimate. Most dissenters disagreed with the Anglican Church only on secondary matters of worship and ecclesiology, and although this was a considered a serious sin, only a few seventeenth century Anglican writers thought that this 'crime' deserved the death penalty. The English Act of Supremacy significantly complicated the matter by securely welding Church and state. The Elizabethan bishop Thomas Bilson was of the opinion that men ought to be "corrected, not murdered", ut he did not condemn the Christian Emperors for executing the Manichaeans for "monstrous blasphemies". The Lutheran theologian Georgius Calixtus argued for the reconciliation of Christendom by removing all unimportant differences between Catholicism and Protestantism, and Rupertus Meldenius advocated in necessariis unitas, in dubiis libertas, in omnibus caritas (in necessary things unity; in uncertain things freedom; in everything compassion) in 1626.

In his book on the English Reformation, the late A. G. Dickens argued that from the beginning of the Reformation there had "existed in Protestant thought in Zwingli, Melanchthon and Bucer, as well as among the Anabaptists a more liberal tradition, which John Frith was perhaps the first to echo in England". Condemned for heresy, Frith was burnt at the stake in 1533. In his own mind, he died not because of the denial of the doctrines on purgatory and transubstantiation but "for the principle that a particular doctrine on either point was not a necessary part of a Christian's faith". In other words, there was an important distinction to be made between a genuine article of faith and other matters where a variety of very different conclusions should be tolerated within the church. This stand against unreasonable and profligate dogmatism meant that Frith, "to a greater extent than any other of our early Protestants", upheld "a certain degree of religious freedom". Frith was not alone. John Foxe, for example, "strove hard to save Anabaptists from the fire, and he enunciated a sweeping doctrine of tolerance even towards Catholics, whose doctrines he detested with every fibre of his being". In the early seventeenth century, Thomas Helwys was a principal formulator of that distinctively Baptist request: that the church and the state be kept separate in matters of law, so that individuals might have a freedom of religious conscience. Helwys said the King "is a mortal man, and not God, therefore he hath no power over the mortal soul of his subjects to make laws and ordinances for them and to set spiritual Lords over them". King James I had Helwys thrown into Newgate prison, where he had died by 1616 at about the age of forty. By the time of the English Revolution, Helwys' stance on religious toleration was more commonplace. While accepting their zeal in desiring a "godly society", some contemporary historians doubt whether the English Puritans during the English Revolution were as committed to religious liberty and pluralism as traditional histories have suggested. However, historian John Coffey's recent work emphasizes the contribution of a minority of radical Protestants who steadfastly sought toleration for heresy, blasphemy, Catholicism, non Christian religions, and even atheism. This minority included the Seekers, as well as the General Baptists and the Levellers. Their witness of these groups together demanded the church be an entirely voluntary, non coercive community able to evangelize in a pluralistic society governed by a purely civil state. In 1644 the "Augustinian consensus concerning persecution was irreparably fractured." This year can be identified quite exactly, because 1644 saw the publication of John Milton's Areopagitica, William Walwyn's The Compassionate Samaritane, Henry Robinson's Liberty of Conscience and Roger Williams' The Bloudy Tenent of Persecution. These authors were Puritans or had dissented from the Church of England, and their radical Protestantism led them to condemn religious persecution, which they saw as a popish corruption of primitive Christianity. Other non Anglican writers advocating toleration were Richard Overton, John Wildman and John Goodwin, the Baptists Samuel Richardson and Thomas Collier and the Quakers Samuel Fisher and William Penn. Anglicans who argued against persecution were: John Locke, Anthony Ashley Cooper, 1st Earl of Shaftesbury, James Harrington, Jeremy Taylor, Henry More, John Tillotson and Gilbert Burnet. All of these individuals considered themselves Christians or were actual churchmen. John Milton and John Locke are the predecessors of modern liberalism. Although Milton was a Puritan and Locke an Anglican, Areopagitica and A Letter concerning Toleration are canonical liberal texts. Only from the 1690s onwards did the philosophy of Deism emerge, and with it a third group that advocated religious toleration. But, unlike the radical Protestants and the Anglicans, the deists also rejected biblical authority; this group prominently includes Voltaire, Frederick II of Prussia, Joseph II, Holy Roman Emperor, Thomas Jefferson and the English Irish philosopher John Toland. Following the debates that started in the 1640s, the Church of England was the first Christian church to grant adherents of other Christian denominations freedom of worship with the Act of Toleration 1689, which nevertheless still retained some forms of religious discrimination and did not include toleration for Catholics. Even today, only individuals who are members of the Church of England at the time of the succession may become the British monarch.

Renaissance, Reformation and witch hunts occurred in the same centuries. Stuart Clark indicates that is no coincidence, that instead, these different aspects of a single age are representative of a world in the process of revolutionizing its way of thinking and understanding. Clark says that understanding one aspect of the age, such as the witch hunts, can lead to a greater understanding of another, such as the development of tolerance. Until the 1300s, the official position of the Roman Catholic Church was that witches did not exist. In medieval canon law, Christian thought on this subject is represented by a passage called the Canon Episcopi. Alan Charles Kors explains that the Canon is skeptical that witches exist while still allowing the existence of demons and the devil. By the mid fifteenth century, popular conceptions of witches changed dramatically, and Christian thought denying witches and witchcraft was being challenged by the Dominicans and being debated within the church. While historians have been unable to pinpoint a single cause of what became known as the "witch frenzy", all have acknowledged that a new but common stream of thought developed in society, as well as in some parts of the church, that witches were both real and malevolent. Scholarly views on what caused this change fall into three categories: those who say the learned in the church spread it, those who say popular tradition did so, and those who say witchcraft was actually being practiced. Of these three possibilities, Ankarloo and Clark indicate the main pressure to prosecute witches came from the common people, and trials were mostly civil trials. In regions that were the most centralized, appellate jurisdictions acted in a restraining capacity, but areas of weak regimes, lacking strong legal or political control, were a disaster for witches. Eventually, Christian thought solidified behind Cautio Criminalis (Precautions for Prosecutors) which was written by Friedrich Spee, in 1631. As a Jesuit priest, he personally witnessed witch trials in Westphalia. Driven by his priestly charge of enacting Christian charity, he describes the inhumane torture of the rack with the graphic language of the truly horrified saying, "it makes my blood boil." As a professor, Spee sought to expose the flawed arguments and methods used by the Dominican witch hunters along with any authority who allowed it, including the emperor. Spee's primary methods for doing so were sarcasm, ridicule and piercing logic. On 7 December 1965 the Catholic Church's Vatican II council issued the decree "Dignitatis humanae" which dealt with the rights of the person and communities to social and civil liberty in religious matters. The Vatican II document Nostra Aetate absolved the Jewish people of any charge of deicide and affirmed that God has always remained faithful to his covenant with Israel. On 12 March 2000, he prayed for forgiveness because "Christians have often denied the Gospel; yielding to a mentality of power, they have violated the rights of ethnic groups and peoples, and shown contempt for their cultures and religious traditions."

After World War II and the Holocaust, many Protestant theologians began to reassess Christian theology's negative attitudes towards the Jews, and as a result, felt compelled to reject the doctrine of supersessionism. But there are also ideals similar to the concept of modern tolerance throughout the history of Christian thought (and philosophy and other religious thought) that can be seen as the long and somewhat torturous "prehistory" of tolerance. The Peace of Westphalia in 1648 included the first statement of freedom of religion in modern history. In the twenty first century, nearly all contemporary societies in the world include religious freedom in their constitutions or other national proclamations in support of human rights. However, at the symposium on law and religion in 2014, Michelle Mack said: "Despite what appears to be near universal expression of commitment to religious human rights, violations of freedom of religion and belief, including acts of severe persecution, occur with fearful frequency." In 2018, the U. S. Department of State, which releases annual reports in which it documents varying types of restrictions which are imposed on religious freedom around the world, detailed country by country, the violations of religious freedom which are taking place in approximately 75% of the 195 countries in the world. This indicates intolerance is more of a social process, tied to social identity, than an ideological one. For example, Christianity in Iraq dates from the Apostolic era in what was then Persia; the U. S. Department of State identified 1.4 million Christians in Iraq in 1991 when the Gulf War began. By 2010, the number of Christians dropped to 700,000 and it is currently estimated there are between 200,000 and 450,000 Christians left in Iraq.