Dennis Prager wrote a great column on exactly that theme a couple years ago:
Of course, the great majority of Muslims are peaceful -- so what?
http://jewishworldreview.com/1102/prager110502.asp
You can skip to the last paragraph or two if you're short on time, but it is not a long column, and worth the read.
That's a good article, and it says it a lot better than I ever could.
I would depart from him in one respect:
I don't care if the Muslim countries blow each other to bits as long as they keep that home grown terror out of America.
The American Muslims are the ones I'm pissed at!