Editor's note: Khairi Abaza is a senior fellow at the Foundation for Defense of Democracies, a a policy institute that aims to promote democracy and address the challenges of terrorism and Islamist politics.
(CNN) -- Since President Hosni Mubarak fell in February, Egypt has become a freer country in many ways. But the ruling military council is continuing his tradition of using the threat of an Islamist takeover to perpetuate a government under which one political force can lord over all others.
Last week, military rulers began a dialogue with organizations and coalitions representing the youth of the revolution, spurred by nationwide protests calling on the military to ratify a new constitution before holding legislative elections. Instead, the military and the Muslim Brotherhood now insist on holding elections in September, and allowing the winners to draft the new constitution.
This is a formula for allowing the Muslim Brotherhood to supplant the military as the arbiter of another authoritarian system. The military council knows well what Western leaders fear when they see the brutal work of largely extremist groups such as the Salafis, who have been involved in a growing number of attacks against Christians and other Muslims in Egypt.
Whether or not they support these attacks, the military leaders may benefit from them politically, as the violence allows less radical but still religious groups like the Muslim Brotherhood to present themselves as more mainstream. This drags the country's political center farther toward the theocratic extremes, worrying Washington.
The Obama administration must make clear that the money it has promised Egypt's transitional government -- $1 billion, plus another billion in loan guarantees -- is tied to ongoing political and economic reforms, including respect for human rights, a truly democratic constitution with checks and balances, equality for all Egyptians under the law and a commitment to a free-market economy. These steps will help keep Egypt from sliding back to despotism.
In late May, the military council declared that remnants of the old regime were sparking sectarian confrontations in hopes of destabilizing the new order. Salafists had recently struck a Coptic church in Imbaba, a poor Cairo neighborhood. They attacked worshippers with clubs, swords and automatic weapons, leaving six Christians and six Muslims dead, and the country in a state of shock.
Shortly afterward, the military arrested scores of Salafis. Members of the Youth of the Revolution made human shields of themselves to protect churches in Imbaba.
The Muslim Brotherhood is trying hard to dissociate itself from the Salafis. In an interview in May on the pro-democracy channel "On TV," Mohamed Habib, a charismatic Muslim Brotherhood reformer and former deputy supreme leader, harshly criticized the Salafis.
Before the revolution, Salafis in Egypt tended to avoid politics. They dedicated their time to prayer and religious study. They were less visible and less vocal than other ultra-conservative organizations, such as the Islamic Group, which was responsible for most attacks on tourists in the 1990s.
The revolution changed that. After Mubarak's ouster, they began to demand that Egypt institute Islamic jurisprudence -- sharia law. Though the Salafis are small in number, and many repudiate violence, they have stoked considerable fear across the country and their ability to move in large numbers and carry out well-organized attacks suggests that they are funded..
The media, including both satellite channels and Egypt's state-owned television outlets, have given the Salafis a great deal of air time to articulate their message, even as they have harassed Coptic Christians, other Muslims and anyone else who does not share their views.
Salafis are now squaring off with the Copts over a Coptic woman who converted to Islam. They claim she is held captive by the Coptic Church. The woman appeared on television next to her husband, declaring that she was still a Christian, asking to be left alone and urging Egyptians to focus on the future of their country. The case is not unique, as Salafis regularly accuse the Coptic Church of kidnapping Christian women who are converting to Islam.
The Salafis' actions are a double-edged sword for the Muslim Brotherhood. On the one hand, they make religious parties look unpleasant and radical. But the Salafi radicals enable the Brotherhood to dissociate itself from more extreme positions, and present itself as a more mainstream and tolerant version of political Islam.
Al-Azhar University, the highest Muslim authority in Egypt, is now trying to form an alliance with the Sufi orders -- Islamic spiritual orders that have several million followers in the country -- to counter the Salafis. Meanwhile, Salafis now threaten to destroy the mausoleums and tombs of Muslim holy men and women, putting them on a collision course with the Sufis. Each Egyptian city is home to at least one saint's tomb, and some attract millions of visitors every year. Some Sufi orders have hundred of thousands of followers, and visiting Muslim holy tombs is deeply enshrined in Egyptian culture. To most Egyptians, destroying them would be blasphemy.
If the Salafis are allowed to continue their attacks, they may ignite a major sectarian conflict, turning Egypt into a source of instability for the whole region.
Of course, the situation may not get that dire, but the question remains: Why are Egypt's new military rulers allowing the Salafists to remain so well funded and above the law? Who benefits from the chaos and fear they are creating? And how much real power will the military cede to Islamists in drafting the new constitution?
In the end, the Muslim Brotherhood may benefit by the Salafists' violence, and the military leaders can use them as a warning to Washington: see what happens when you don't keep us bought?
The opinions expressed in this commentary are solely those of Khairi Abaza.