Before Philpot was burned at the stake in 1555, he was able to vindicate his decision to spit on a fellow Protestant martyr. He wrote a tract with a long and lively title: An Apology of John Philpot; written for spitting upon an Arian: with an invective against Arians, the very natural children of Antichrist: with an admonition to all that be faithful in Christ, to beware of them, and of other late sprung heresies, as of the most enemies of the gospel.

Less than two years before the spitter Philpot was burned alive by Catholics, another Protestant, Michael Servetus, had suffered the same fate at the hands of fellow Protestants in Geneva. Servetus also denied the doctrine of the Trinity, and this, along with his repudiation of infant baptism (both were capital crimes), brought about the trial of Servetus on thirty‐​nine counts of heresy and blasphemy and for attempting “to infect the world with stinking heretical poison.” It took thirty minutes for Servetus to die as he was roasted over a slow fire.

The burning of Servetus became a cause célèbre among Protestants. His execution was engineered by John Calvin, the most influential Protestant of the time, and it was subsequently defended by other leading Protestants. But this acclaim was far from unanimous. Some Protestants with liberal tendencies, most notably Sebastian Castellio, condemned the execution of Servetus, thereby sparking a debate that became a watershed in the history of religious toleration.

Servetus became a poster boy in the struggle for religious toleration, but he was a problematic one by modern standards. As much as we might like to think that Servetus was a champion of religious freedom who was victimized by his intolerant adversaries, this was by no means the case. Although Servetus was more tolerant than Calvin and many of their contemporaries, he was not himself a champion of religious freedom. On the contrary, Servetus maintained that heretics who are “incorrigible and obdurate in their wrong” should be put to death, while more moderate punishments, such as banishment, should be imposed in less severe cases. During his trial in Geneva, Servetus insisted that his adversary John Calvin was the one who should suffer the ultimate penalty for heresy.

These stories about Philpot and Servetus illustrate a recurring problem in the broader story of religious freedom, namely, that the victims of intolerance were often intolerant themselves and would not have recognized the rights of those whom they regarded as the real heretics. Moreover, during the seventeenth century many illustrious Protestant defenders of toleration, such as John Milton and John Locke, excluded atheists and Catholics from their arguments for freedom of conscience; and Catholic proponents of toleration typically made major exceptions as well, especially where heretics and schismatics were concerned. Only among a handful of these early defenders of toleration, such as the English Levellers and Roger Williams (the founder of Rhode Island), do we find arguments for a comprehensive religious freedom that included believers and nonbelievers of every stripe.

It was because defenses of toleration were so frequently riddled with exceptions that the word itself acquired a bad reputation among some eighteenth‐​century proponents of religious freedom. In 1785, the English minister and libertarian Richard Price discussed “liberty of conscience”—a term that had been used for around 250 years—but he distinguished between liberty of conscience and religious toleration. “In liberty of conscience,” wrote Price in Observations on the Importance of the American Revolution, “I include much more than toleration…. Not only all Christians but all men of all religions ought to be considered by a state as equally entitled to its protection as far as they demean themselves honestly and peaceably.” In a political context, to “tolerate” religious beliefs and practices is sheer presumption, because it implies that a government grants religious freedom to people as a privilege, favor, or for reasons of state. In contrast, Price insisted that liberty of conscience is a natural and inalienable right that governments have a duty to respect. It is a sphere over which governments have no legitimate jurisdiction, so it is not something they can choose to tolerate or not.

Similarly, during a session of the French Constituent Assembly (which passed the Declaration of the Rights of Man in 1789), Mirabeau declared that he would not “preach toleration” because it suggests an authority with the power to tolerate those beliefs that it deems acceptable, and this implies a power not to tolerate as well. Hence the very notion of toleration conveys “a suggestion of tyranny” because it is inconsistent with the sacred right of individuals to the “unlimited freedom of religion.”

A few years later, in Rights of Man, Thomas Paine also condemned the idea of toleration, calling it a “counterfeit form” of intolerance: “Both are despotisms. The one assumes to itself the right of withholding Liberty of Conscience, and the other of granting it.” Paine praised the new French Constitution for abolishing toleration (and intolerance along with it) and establishing instead the “universal right of conscience.”

This contrast between toleration and the right to freedom of religion reflected a radical development in political theory that may broadly be described as libertarian. Although elements of this approach, such as its emphasis on natural law, had affinities with traditional political ideas (some of which can be found in the philosophers of ancient Greece), an integrated libertarian theory did not begin to take shape until the early 1600s. It arose largely in response to modern theories of absolutism, which stressed the absolute sovereignty of the state (as embodied in a monarch). Individualists, in contrast, argued that self‐​sovereignty—as manifested in the natural and equal rights of individuals—is the only legitimate basis for political power. From this foundation there arose various theories to explain how governments acquire legitimate political power through a process of consent, whereby the rights of individuals (or the power to enforce them) are delegated to a ruler.

The more radical of these social contract theories (as they are commonly known) were political dynamite, for they insisted that all rights, including those rights claimed by a government, are ultimately the rights of individuals. This approach struck at the heart of theories of absolute sovereignty by imposing severe limitations on what a government may legitimately do. If, for instance, a government claimed the right to regulate the religious beliefs and practices of its people, it was necessary to show, first, how that right could be possessed by individuals in a society without government (a “state of nature”); and, second, how that right could have been voluntarily delegated to a government.

These libertarian developments in political theory were closely related to the struggle for religious freedom. This is not a judgment made with the wisdom of hindsight; it is something that leading theorists and historians of classical liberalism have emphasized for over two centuries. When, in 1866, John Stuart Mill characterized “liberty of conscience” as “the first of all the articles of the liberal creed,” he was echoing a belief that had been stated many times before. Even when James Madison, writing in 1792, characterized freedom of conscience as the most “sacred” of all rights, he was merely restating a tenet that originated long before he was born.

Liberty of conscience—this expression, which appears to have originated in the early 1500s, is a dominant and recurring theme throughout the struggle for religious freedom. But it has implications that extend beyond the realm of religion. When Herbert Spencer and other nineteenth‐​century libertarians protested against schemes of government welfare, they argued that charity should be a matter of conscience, as determined by each individual, and that charity has moral worth only when it is given voluntarily.

Similarly, when English Dissenters (i.e., Baptists, Congregationalists and other Protestants who did not belong to the Anglican Church) waged a vigorous campaign against schemes for state education, they insisted that education, whether religious or secular, is a matter of conscience and therefore not a legitimate function of government. Arguments for freedom of speech and press—and even for free trade, which entails the right to dispose of one’s property as one sees fit—were frequently based on the same moral premise.

This is why an understanding of the history of religious freedom is essential to understanding the history of freedom in other spheres. It was during the struggle for religious freedom that “liberty of conscience” was transformed from a vague battle cry into a sophisticated political theory based on natural rights. The sphere of conscience became the realm of human action where private judgment should reign supreme—a sphere where coercion, whether exercised by government or individuals, is morally improper. And as this sphere was progressively extended beyond religious beliefs and practices to more secular concerns, the proper role of government receded from the many “positive” functions it had exercised in previous centuries to the “negative” function of protecting individual rights.