Two: I'm willing to give you that Clinton was not responsible for the state of the economy during his turn, supply-side did that. However, I find it hard to accept that a two-year liberal congress was able to do more damage to our economy than a 6-year colonial/neo-imperial effort in the Middle-East.
1) Because of the unique situations of each, Islamic extremists tend to feel more compelled to use violent means to attain their religious dictates, whereas the societies in which Christian extremists operate tend to more harshly censure violence. I have no doubt, though, that a Jerry Falwell or a Pat Robertson would be utterly willing to advocate violent means for enforcing their religious mandate if they saw at as being in their beneficial (in fact, we can see examples of publicly less-renowned Christian extremists engaging in a wide range of terrorist activities, from bombing abortion clinics, to lighting crosses on the yards of "darkies").
2) The other difference, and I'm sure that many in America find it hard to admit that we largely do make this distinction, is that the Christian extremists are, generally speaking, "white" and the Muslim extremists are, generally speaking, not. Just as in nearly every single bit of public discourse on any matter relating to foreign policy (and this certainly qualifies) in the US, race is a primary factor in our calculations, even though social changes in the 1960's make us uncomfortable with admitting it.
This certainly doesn't cover EVERYTHING, but these are the two primary differences that play a major factor in how Americans, in general, relate to these two groups.
There are three kinds of people: men, women, and unix.