The Muslim Brotherhood (MB) is an important part of the Egyptian political landscape, a leading opposition force that was previously represented in parliament (before the ruling NDP party put its vote-rigging habit on steroids in last elections - November, 2010). The MB neither initiated nor led the current round of protests, but they have joined them and are likely to be a prominent player in a democratic Egypt (neither a dominant nor marginal role seems most likely).
The ability to use the Islamist boogieman to fuel US fears draws on a combination of unfamiliarity and ignorance, cultural arrogance, and real policy differences on regional issues, notably on Israel. That Arab publics left to their own devices should freely choose to support religious conservatives should largely be none of our business: Americans in many states make a similar choice at the ballot box. That American policymakers have so few links into the MB or serious channels of communication is simply a failure of American policy.
Nathan Brown, an expert on Islamist parties, has warned against US policymakers being misled by a tendency towards "Ikwanophobia" (ikwan is Arabic for the Muslim Brothers' movement). One cannot support participatory democratic politics in the Arab world while being totally allergic to the role that democratic Islamists will play. These movements are part of the legitimate political mix. They are more often than not at loggerheads with Al Qaeda, and far from being Al Qaeda-lite, they are frequently the most effective bulwark against Al Qaeda-style extremism.