The “freedom of conscience” is, as Prof. Steven Smith has observed, “central to the modern discourse of religious freedom” and, indeed, “to the modern self-understanding generally.” This “modern” centrality is not a recent innovation. It is clear that the freedom of conscience was at the heart of many Americans’ thinking at the Founding about religious liberty and church-state relations. “Liberty of conscience,” Prof. John Witte has explained, “was the general solvent used in the early American experiment in religious liberty. It was almost universally embraced in the young republic—even by the most rigid of establishmentarians.” According to Prof. Noah Feldman, the Founding-era commitment to conscience was the “principled reason” for the proposal and ratification of the First Amendment’s free-exercise and no-establishment clauses.

In fact, as Witte has shown, the liberty of conscience was one of several related “essential rights and liberties of religion” cherished by the Founding generation. Others included the “separation of church and state” and the “disestablishment of religion.” It is and has long been widely believed that these latter principles both reflect and reinforce our commitment to conscience. Justice Souter, for example, wrote recently that the rule against public spending in direct support of religion, which the Court found in the no-establishment clause, “translates into practical terms the right of conscience.”

How, though, does this relationship work? That is, how, precisely, do the anti-establishment norm and the “separation of church and state” vindicate the freedom of conscience? We know that Roger Williams—the founder of the colony of Rhode Island and a fierce and fiery critic of the “soule rape” of religious persecution—connected the protection of conscience with the maintenance of a wall between the “Garden” of religious faith and the “Wilderness” of civil power and public affairs. But again, how exactly does this wall, this separation, protect the “soule,” the seat of conscience?

The “separation of church and state,” it turns out, is a powerful structural principle; it is a principle of pluralism, of multiple and overlapping authorities, of competing loyalties and demands. It is a rule that limits the state (not a program of marginalizing or privatizing religion) and thereby clears out and protects a social space, within which persons are formed and educated, and without which the liberty of conscience is vulnerable. The no-establishment rule, then, protects the liberty of conscience primarily by respecting and protecting the independence of non-state authority.

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Now, there are at least four other ways—more obvious and familiar ways, perhaps—that we might think that church-state separation shores up the liberty of conscience.

First, and most obviously, we could say that the First Amendment does not permit coerced prayers or professions of faith. Justice Anthony Kennedy emphasized this fact in Lee v. Weisman, the Supreme Court’s 1992 graduation-prayer case. “One timeless lesson,” he wrote, “is that, if citizens are subjected to state-sponsored religious exercises, the State disavows its own duty to guard and respect that sphere of inviolable conscience and belief which is the mark of a free people.” Certainly, we should say this much (even as we acknowledge that it will often be a challenge to identify “coercion”). However, this no-coercion rule is better regarded as an implication of the Free Exercise Clause. After all, there is no necessary connection between “establishments” of religion and “coerced” religious observance, while such coercion seems the paradigmatic violation of any plausible understanding of the “free exercise” of religion.

Second, we might think that the no-establishment rule protects conscience by outlawing government actions or expression that “endorse” religion, sending—in Justice O’Connor’s words—a “message to non-adherents that they are not full members of the political community.” This theory is often at work in cases and controversies surrounding public displays and monuments—the Ten Commandments, for example, or a holiday display. And it is true that the messages such displays and symbols communicate might well, in some cases, be in tension with a deep commitment to political and civic equality, or with the proper regard for the sensitivities of fellow citizens. But again, these cases seem some distance removed from the liberty of conscience. There are many good reasons to worry, in a pluralist society, about excessive endorsements of religion (just as there are reasons to worry about excessive hostility or sensitivity to religious expression in the public square or official acknowledgment of religious traditions). But the policing by judges of holiday displays, in the name of non-establishment, protects conscience—if at all—only indirectly.

Third, it could be that the no-establishment rule protects conscience by limiting so-called “morals legislation,” and by requiring that all laws passed and demands made by the civil authority have what the Court calls a “secular purpose,” rather than a religious one. Justice Stevens, for example, has often suggested that laws regulating abortion, or laws outlawing physician-assisted suicide, are unconstitutional because they involve the imposition of religious beliefs, and therefore burden the freedom of conscience. Similarly, some have suggested that political resistance to same-sex marriage is in tension with the no-establishment rule—and so also with our commitments to conscience and equal liberty—because the reasons for this resistance rest in religious teaching rather than public reason.

There are good reasons—indeed, there are religious reasons—to avoid overreaching when it comes to morals legislation. After all, it was not only John Stuart Mill, but also St. Thomas Aquinas, who believed that the law should neither require every virtue nor outlaw every vice. Wholly and apart from the Establishment Clause’s requirements, the law ought to allow the greatest space possible for freedom—even when that freedom is not exercised in accord with moral truth—consistent with the demands of public order. It is a mistake, though, to frame the morals-legislation debate in terms of church-state separation and liberty of conscience. The disestablishment of religion does not limit the kinds of reasons that citizens and legislators may deploy when debating the proper use of the police power, and the constraints on morals legislation to which the political authority should submit are not tethered to church-state separation.

A fourth way has loomed large in our history and constitutional law. It has often been argued—including by Justices of the Supreme Court—that financial support by the government for religious institutions or activities violates the conscience of those who are compelled to contribute, though taxes, to the public purse. As Thomas Jefferson famously put it, “to compel a man to furnish contributions of money for the propagation of opinions which he disbelieves is sinful and tyrannical.” A similar view motivated James Madison to pen his famous Memorial and Remonstrance against Religious Assessments, and to insist that conscience is offended by any law that would “force a citizen to contribute three pence . . . or the support of any establishment.”

This view, despite its pedigree, is also mistaken. The no-financial-aid-to-religion rule—to the extent it still exists—is not how church-state separation in fact protects and nurtures the formation and freedom of conscience because the expenditure of public funds does not, in fact, meaningfully burden the “conscience” of taxpayers. As a Massachusetts judge wrote, in 1810, in response to the claim that “when a man disapproves of any religion, . . . to compel him by law to contribute money for public instruction in such religion or doctrine, is an infraction of his liberty of conscience,” this objection “seems to mistake a man’s conscience for his money and to deny the state a right of levying and appropriating the money of the citizens, at the will of the legislature, in which they are all represented.”

It is reasonable to ask why we should think, even if James Madison thought, that the freedom of conscience is unjustly burdened, and the Religion Clauses therefore violated, simply by the use of public funds raised through taxes to pay for, say, scholarships for poor children attending Catholic schools. Such expenditures do not present, really, an “establishment” of religion like those with which those who ratified the First Amendment, and debated religious liberty in the late 18th century were familiar. True, Jefferson’s above-quoted objection packs a lot of rhetorical weight, but it is not reflected at all in the reality of politics and government today. Every taxpayer furnishes money for the “propagation of opinions which he disbelieves.” Indeed, every taxpayer pays for all kinds of government actions to which they have serious objections in conscience. At the end of the day, as Steve Smith has observed, good explanations simply have not yet been given “for why the burden on conscience applies when a taxpayer objects . . . to expenditures that may benefit religion but not when a taxpayer objects on religious or conscientious grounds to expenditures that run contrary to the taxpayer’s beliefs.”

In sum, the no-establishment rule does protect the liberty of religious conscience, but not in the way, or ways, that we usually think.