Freedom of speech doesn't just protect mainstream political thought, it protects all.
To limit what can be said about a religion, or a political party, or even a race, is foolish.
The Muslims have a right to say what they believe, and so do we, we will disagree, we might both be offended, but the alternative is not to talk at all about anything of substance.
They have no right never to be offended, I'm offended by peoples political and religious positions on an almost daily basis, often by people I'm friendly with.
It's no reason to riot.
As for the religion in politics thing, I don't hear many people proposing making membership in a religion a disqualifier for public office or denying the religious their right to free speech. What I do see a great deal of, and rightly so, is people demanding that they keep their religion out of the LAW.
If you're going to write legislation, there should be a rational basis for it, not a religious one, and it should be constitutionally sound.
If you want to pray in congress or whatever that's fine with me.