Bruce Riedel says we shouldn't worry overly much about the possibility of the Muslim Brotherhood joining a post-Mubarak government. I reserve the right to worry, but Riedel makes an interesting argument:

The Egyptian Brotherhood renounced violence years ago, but its relative moderation has made it the target of extreme vilification by more radical Islamists. Al Qaeda's leaders, Osama bin Laden and Ayman Zawahiri, started their political lives affiliated with the Brotherhood but both have denounced it for decades as too soft and a cat's paw of Mubarak and America.
Egypt's new opposition leader, former International Atomic Energy Agency head Mohamed ElBaradei, has formed a loose alliance with the Brotherhood because he knows it is the only opposition group that can mobilize masses of Egyptians, especially the poor. He says he can work with it to change Egypt. Many scholars of political Islam also judge the Brotherhood is the most reasonable face of Islamic politics in the Arab world today. Skeptics fear ElBaradei will be swept along by more radical forces.

Israel, of course, isn't looked on favorably by the Brotherhood:

The most problematic issue between the Ikhwan and America will be Israel. The Brotherhood raised an army to fight Israel in its war of independence in 1948. Its Palestinian branch was the nucleus for Hamas, and the Brotherhood retains links to the rulers of Gaza. The Ikhwan's leaders understand the peace treaty with Israel is the cornerstone of modern Egyptian foreign policy and underwrites America's $2 billion annual aid as well as the lucrative tourist trade, but they are very critical of Israel, its leader, and policies. Their base is fundamentally opposed to any Egyptian cooperation with Israel.