A more direct rebuke to the supposedly divine and exclusive origins of the Church of England—or any other national church—could hardly be conceived. At the same time, Locke’s reputation as a radical individualist is misplaced. Voluntary participation in a faith community is not an evasion of one’s moral duties. Rather, the public worship of God, according to the dictates of conscience, is the means by which these duties are to be carried out.

Locke’s commitment both to voluntary religion and voluntary, contractual government are mutually reinforcing. Just as people join and remain in religious communities by their consent, so they enter and sustain political communities. “Men being, as has been said, by Nature all free, equal, and independent,” Locke writes in the Second Treatise, “no one can be put out of this estate and subjected to the political power of another without his own consent.” If the members of a faith community believe their church is failing to uphold its spiritual responsibilities, they have a right to leave—without fear of reprisal. Likewise for a political society: If its members believe the political authority is failing to safeguard their natural rights—their “lives, liberty, and estates”—it forfeits the right to govern.

There is no daylight between the positions staked out in A Letter and The Two Treatises over the obligations of a just government toward its citizens. “It is the duty of the civil magistrate, by the impartial execution of equal laws,” he writes, “to secure unto all the people in general, and to every one of his subjects in particular, the just possession of these things that belong to this life.” Political rulers who ignore this duty and violate the natural rights of their subjects—including the liberty to worship God according to conscience—lack legitimacy. After a “long train of abuses,” they “put themselves into a state of war with the people.” Once that happens, the people may withdraw their consent. No wonder the American Founders ranked Locke as among the greatest of modern philosophers.

The ongoing turmoil in the Middle East and North Africa has confirmed Locke’s insight many times over. A groundbreaking 2002 Arab Human Development Report, written by a group of Arab intellectuals, admitted that a “freedom deficit” in Muslim societies threatened the development and stability of the entire region. That deficit remains, and repression and violence on the basis of religious identity lie near the heart of the problem. Blasphemy laws, anticonversion laws, laws restricting freedom of worship, institutionalized discrimination, mob violence against religious minorities—these are the norms in many Muslim-majority countries. Shia and Sunni Muslims are most often the victims, but Jews, Christians, Baha’is and Alevis face increasing threats against their communities, even extinction.

In Locke’s world—as in much of ours—religion and politics were deeply intertwined. Thus Locke sought to reform the Christian church as a prelude to a social revolution that would curb the hatreds inspired by militant religion. “It is not the diversity of opinions which cannot be avoided,” he writes, “but the refusal of toleration to those that are of different opinions, which might have been granted, that has produced all the bustles and wars that have been in the Christian world, upon account of religion.”

Locke also sought to reform the state, so that it would protect the right of every individual—regardless of religious identity—to pursue his obligations to God according to the dictates of conscience. Locke’s vision of a just society would extend political equality and religious freedom to all Christian sects, as well as to religious believers of all kinds:

But those whose doctrine is peaceable, and whose manners are pure and blameless, ought to be upon equal terms with their fellow-subjects. Thus if solemn assemblies, observations of festivals, public worship be permitted to any one sort of professors, all these things ought to be permitted to the Presbyterians, Independents, Anabaptists, Arminians, Quakers, and others, with the same liberty. Nay, if we may openly speak the truth, and as becomes one man to another, neither Pagan, nor Mahometan, nor Jew, ought to be excluded from the civil rights of the commonwealth, because of his religion. The gospel commands no such thing.

On Locke’s list are some of the most despised religious minorities of seventeenth-century Europe. Unlike his contemporaries, he does not regard them as threats to civic peace. Thus the anti-Semitism that kept Jews on the margins of European society is rejected. “If a Jew does not believe the New Testament to be the word of God,” he writes, “he does not thereby alter any thing in men’s civil rights.” Elsewhere in the Letter, Locke disparages English laws prohibiting the construction of synagogues and limiting the Jews to private worship.

If we allow the Jews to have private houses amongst us, why should we not allow them to have synagogues? Is their doctrine more false, their worship more abominable, or is the civil peace more endangered, by their meeting in public, than in their private houses?

Not even Muslims, whose status among Europeans was always problematic, should be denied basic civil liberties. If we recall that Muslim-Christian relations hit a new low after the Battle of Vienna in 1683—two years before Locke wrote his Letter—we discover in Locke a remarkable egalitarianism. In his groundbreaking work, John Locke, Toleration and Early Enlightenment Culture, John Marshall draws attention to Locke’s unconventional aims: “In most Christian eschatological schemes of the seventeenth century,” he writes, “the Jews were to be converted and ‘the Turks’ destroyed.”

Locke is often accused of sharing the anti-Catholic hatreds typical of English Protestants, but a careful reading of his Letter suggests otherwise. In explaining why religious beliefs should not come under the jurisdiction of the magistrate, Locke uses Catholicism as a test case: “If a Roman Catholic believes that to be really the body of Christ, which another man calls bread, he does no injury thereby to his neighbor.” Provided they did not try to subvert the political order, Catholics deserved equity under the law.

How did Locke hope to bring about a more tolerant society? Civil law was important, but unable by itself to establish a more generous political regime. Locke believed that religious leaders played a critical role in changing cultural norms; they must use their pulpits to promote a spirit of mutual regard in civil society.

In Locke and Modern Life, political scientist Lee Ward emphasizes the cultural task of religious communities under Locke’s vision. The churches, Ward writes, must “place the great incentive of divine judgment behind the cause of toleration rather than against it.” In his Letter, Locke admonishes church leaders against offering only a grudging toleration toward those with different religious views. “We must not content ourselves with the narrow measures of bare justice: charity, bounty, and liberality must be added to it,” he writes. “This the gospel enjoins, this reason directs, and this that natural fellowship we are born into requires of us.”

Europe’s coercive policies to achieve religious conformity had run their course; they failed to produce either social unity or authentic faith. Rather, government’s abusive treatment of unpopular religious groups turned citizens into lawbreakers and worshippers into hypocrites. “No peace and security, no, not so much as common friendship, can ever be established or preserved amongst men, so long as this opinion prevails . . . that religion is to be propagated by force of arms.” Locke turns Hobbes’s Leviathan on its head. Political absolutism—and the suppression of dissent that went with it—was far more likely to produce chaos and social disintegration than a “just and moderate government.”

The social consequence of Locke’s defense of toleration is religious pluralism. Under a system of impartial justice, it will become the key to civic peace and political stability.

It is often forgotten that beneath Locke’s plea for a more just and tolerant society flowed a river of rage: a fierce resentment at the hypocrisy and violence that had scandalized the Christian church. Locke’s strategy was to reinterpret the Christian faith—to leverage the moral authority of Jesus—to instigate a massive restructuring of political and ecclesiastical life.

COULD SOMETHING like this take root in Muslim societies? There are hopeful signs: a growing sense of outrage among Muslims at the atrocities being committed under the banner of Islam. This helps to explain the remarkable influence of Pakistan’s Malala Yousafzai, the teenager shot in the head by the Taliban for her crusade to allow women to go to school. She not only survived the attack but also refused to remain silent about women’s rights—and in her defiance has created a mass movement of like-minded reformers.

“There are hundreds of human rights activists and social workers who are not only speaking for their rights, but who are struggling to achieve their goal of peace, education and equality,” she told a spellbound audience at the United Nations.

So here I stand, one girl among many. I speak not for myself, but so those without a voice can be heard. . . . We cannot all succeed when half of us are held back. We call upon our sisters around the world to be brave, to embrace the strength within themselves and realize their full potential.