For a very long time, Protestant leaders were those referees. If individual impiety flourished in centuries past, churches still wielded significant control over civic culture: the symbols, standards and sexual mores that most of the populace respected in public, if not always in private. Today, more and more Americans openly accept extramarital sex, homosexuality and other outrages to traditional Christian morality. They question the Protestant civil religion that has undergirded our common life for so long.

The idea of Protestant civil religion sounds strange in a country that prides itself on secularism and religious tolerance. However, America’s religious free market has never been entirely free. The founding fathers prized freedom of conscience, but they did not intend to purge society of Protestant influence (they had deep suspicions of Catholicism). Most believed that churches helped to restrain the excesses of mob democracy. Since then, theology has shaped American laws regarding marriage, public oaths and the bounds of free speech. For most of our history, the loudest defenders of the separation of church and state were not rogue atheists, but Protestants worried about Catholics seeking financing for parochial schools or scheming their way into public office to take orders only from mitered masters in Rome.

Activists on both the left and the right tend to forget this irony of the First Amendment: it has been as much a weapon of religious oppression as a safeguard for liberty. In the 19th and early 20th century, when public school teachers read from a Protestant translation of the Bible in class, many Americans saw benign reinforcement of American values. If Catholic parents complained, officials told them that their Roman dogma was their own private concern. The underlying logic here was not religious neutrality.

The Protestant bias of the American public sphere has mellowed over time, but it still depends on “Christian secularism,” said Elizabeth Shakman Hurd, a political scientist at Northwestern University. This is a “political stance” premised on a “chiefly Protestant notion of religion understood as private assent to a set of propositional beliefs,” she told me. Other traditions, such as Judaism and Islam and to some degree Catholicism, do not frame faith in such rationalist terms, or accept the same distinction between internal conviction and public argument. The very idea that it is possible to cordon off personal religious beliefs from a secular town square depends on Protestant assumptions about what counts as “religion,” even if we now mask these sectarian foundations with labels like “Judeo-Christian.”

Conservative Christian activists hold those sectarian foundations more dearly than they admit, and they are challenging the Obama administration’s efforts to frame access to contraception and same-sex marriage as civil rights immune to the veto of “private” conscience. Alan Sears, president of the legal advocacy organization Alliance Defending Freedom, sees an unprecedented threat to religious liberty in the harsh fines facing employers who refuse to cover contraception in their insurance programs. “It is a death penalty. It is a radical change,” he told me. “It’s one thing when you’re debating about public space, but it’s another when you say, if you don’t surrender your conscience, you’re out of business.”

Barry Lynn, the director of Americans United for Separation of Church and State (an organization that until 1972 was named, tellingly, Protestants and Other Americans United for Separation of Church and State), sees things differently. He worries about what might happen if an unpredictable Supreme Court agrees to hear conservative Christians’ challenges to the contraception mandate, or their pleas for exemptions for charities that accept federal grants but discriminate on the basis of religion in hiring. “The court could create something vastly more dangerous than corporate free speech: a ‘corporate conscience’ claim,” Mr. Lynn, a lawyer and an ordained minister, told me. “These cases could become as significant for the redefinition of religious liberty as Roe v. Wade was a rearticulation of the right to privacy.”

These legal efforts are less an attempt to redefine religious liberty than a campaign to preserve Christians’ historic right to police the boundary between secular principles and religious beliefs. Only now that conservative Christians have less control over organs of public power, they cannot rely on the political process. Now that the “nones” are declaring themselves, and more Americans — including many Christians — see birth control as a medical necessity rather than a sin, Mr. Sears sees a stark course of action for the Catholic and evangelical business owners he represents: “Litigation is all that our clients have.” Their problem, however, is more fundamental than legal precedent. Their problem is that America’s Christian consensus is fragmenting. We are left groping for something far messier: an evolving, this-worldly, compromise.