Tim has already dealt ably with the intolerance being displayed by Republican congresspeople who are freaking out that Muslims have advocacy groups that represent them on the Hill. Marc Lynch and Spencer Ackerman make a separate but still important point that this kind of anti-Muslim bigotry undermines national security by sending the message that Muslims aren't actually welcome in American society -- not just in the Democratic process, but period. Lynch points out that Muslim nations will be less likely to cooperate with a U.S. that seeks to treat all of its Muslim citizens as potential fifth columnists, and Ackerman wrote back in 2005 about how the combination of American pluralism and openness was preventing American Muslims from being radicalized.
I want to briefly make another point. One of the advantages America has in the war on terrorism is that our law enforcement and intelligence agencies can potentially draw on the talents and experiences of Americans who are Muslim or whose families have cultural or ethnic origins in Muslim countries, who have the kind of linguistic and cultural backgrounds that are all too scarce in U.S. agencies at the moment. Political stunts alienate the very communities whose help the government needs in order to effectively protect national security.
-- A. Serwer