Since the Arab Spring began last December, Western analysts have voiced a recurrent fear: that a long era of Arab stability will be replaced not by secular democrats but by Islamic theocrats.

In Egypt, they warn, the Muslim Brotherhood will overtake the young secular activists who bravely brought down dictator Hosni Mubarak. In Syria, they have claimed, Bashar al-Assad’s dictatorship may be brutal, but it is a lesser evil than a Sunni majority that will oppress Christians, Shiites, and women. Such anxiety plays perfectly into the ruling rationale of the region’s secular sultans, who have resisted popular governance with the argument that it spells theocracy.

But such fear and false choices should be resisted. A stable Middle East will be achieved not through the suppression of religion but through its robust inclusion in politics.

The choice facing Arab Spring nations at this point isn’t one between religion and secular government. It’s a choice between democracy that includes all parties – religious and secular – and a regime that imposes a rigid and exclusive secularism.

By allowing religious parties to have political participation, is there a risk that such groups will win some votes and acquire some political power? Yes. The question, though, is not whether such groups oppose liberal democracy and threaten stability – some surely do – but which kind of political environment mitigates their extremist tendencies. And which kind intensifies them.

America's policy of negative secularism

The reflexive fear of politically active religious groups is rooted in an ideology of secularism that persists among elite American foreign policy makers. Now, if secularism means a healthy distinction between religious and political authority, it is essential to democracy. Pope Benedict XVI called this “positive secularism.”

Negative secularism, by contrast, presumes that religion is irrational, premodern, violent, and headed for extinction – and has no place in democratic politics. Negative secularism mistakenly equates religious political participation with religious takeover and the subversion of democracy. Its answer to theocracy is "seculocracy:" the absolute supremacy of nonreligious principles in politics.

Pro-government forces in Syria illustrated the attitude of seculocracy last week in Hama after they crushed protests there. They scrawled on the walls of the city such slogans as: "No God but al-Assad" and "God falls down and Assad lives."

During the cold war, negative secularism undergirded America’s policy in the Middle East. America’s overriding concern was finding reliable allies against the Soviets. In a few cases these allies were highly religious, as were Saudi Arabia and Pakistan. Far more often, though, they were regimes built on nationalism, economic and social modernization – and the secular containment of grassroots Islam.

From Tangiers to Tehran, such regimes sought to control Islam by marginalizing, privatizing, and sharply regulating it. They gave legal and financial support to approved moderate Muslims; they jailed and tortured traditional dissident Muslims.

When Western liberals questioned why Mr. Mubarak imprisoned 20,000 of his Egyptian citizens, Mubarak replied: It’s either me or the Muslim Brotherhood. The US bought the argument. Such thinking partly explains why the Obama administration was slow to abandon Mubarak. Only days before the dictator’s downfall, according to The New Yorker’s Ryan Lizza, a White House official summarized Mubarak’s message to the US as “Muslim Brotherhood, Muslim Brotherhood, Muslim Brotherhood.”

Repressive secular regimes foster religious extremism

In the end, however, America’s policy of promoting secular dictatorships has simultaneously undermined democracy and stability and bolstered religious radicals. Instead, the United States will best advance its long term interests by encouraging the Middle East’s transitioning regimes to invite all nonviolent religious groups into the political arena.

To be sure, the region contains many unsavory religious groups. Some advocate a harsh form of sharia that denies the rights of women and minorities, calls for the destruction of Israel, and declares America an enemy. Factions within Egypt’s Muslim Brotherhood think along these lines, as do even more extreme Salafists.

But the growth of extremist religious groups is less likely within a political structure that includes, rather than excludes, them. In our recently published book, "God’s Century: Resurgent Religion and Global Politics,” we present evidence that religious groups are most likely to become radicalized and violent when they live under regimes that deny them autonomy and political participation.

America’s longtime friend, the shah of Iran, epitomized the dangerous relationship between repressive secularism and Islamic radicalism. The shah’s harsh repression and manipulation of Iran’s ayatollahs helped turn many of them from quiet political indifference to violent militancy, generating the revolution of 1979 and all of the continuing challenges the Islamic Republic poses to American interests.

The dynamic is similar for religious terrorist groups that have arisen in the ensuing years. Overwhelmingly Islamic, these groups were incubated largely by the repressive policies of America’s Arab and South Asian allies, most of which were secular.

Inclusion sets the ground for peace, partnership

Conversely, we find that religious groups are most likely to be peaceful and supportive of democracy when they live under regimes that respect their autonomy. Islamic countries as diverse as Bangladesh, Indonesia, Malaysia, Mali, Senegal, and Turkey demonstrate that when Islamic parties participate in politics they not only operate by the rules of the democratic game but also, in time, become more moderate.

Moderate Islam also exists in today’s Middle East. While some Egyptian Muslims have attacked Coptic Christians, others have formed protective prayer chains around Coptic churches. Today, a popular Muslim Brother is running for Egypt’s presidency on an independent platform of liberal democratic principles – even to the point of provoking his formal expulsion from the Brotherhood.

Earlier this summer, the US government resumed formal contact with the Egyptian Muslim Brotherhood. This, in our view, suggests a positive turn toward a policy of religious engagement. If the United States wishes to advance democracy, stability, and the defeat of terrorism in the upheaval in the Middle East, it must continue to abjure the brand of secularism that views religion only as a threat. It must realize not only that religion is here to stay but also that, in the right kind of setting and through the right kind of policies, religion can become an ally, not an enemy, of American interests and ideals.

Daniel Philpott is an associate professor of political science and peace studies at the University of Notre Dame. Timothy Shah is associate director of the Religious Freedom Project at Georgetown University’s Berkley Center for Religion, Peace & World Affairs. Monica Duffy Toft is associate professor of public policy at Harvard’s Kennedy School of Government and director of the Initiative on Religion in International Affairs.