Don't assume too much. "24" has started before with politically incorrect villains, only to have the ultimate bad guys wind up being the typical oil/corporate interests. And just a few minutes ago, a new white villain came forth on the show.
So don't discount the possibility that, in the end, the Muslims bad guys will just be the underlings for some Right Wing militia, or something stupid like that.
But otherwise, yes Fox should be commended for getting it right so far at least.
I can see it now: they are all employed by Halliburton!