You know, the lot of you pointing fingers and screaming "Christian hater!" are lying to yourselves. Most of the arguments here are NOT (for added effect, if you're dense ---NOT) about hating christianity.
Many of those, including myself, I'm sure, who bring up problems within the christian religion merely seek to point out that extremists exist in many ways, shapes, and forms. In addition, they should not be considered to be representative of the whole. Just as Timothy McVeigh, Terry Nichols et al. are not representative of the entirety of the Republican party, and instead only a select radical flank of the whole, the muslims who are associated with al-qaeda are radicals and not representative of the whole. Fred Phelps? Radical.
Christianity is a convenient comparison because it is, like Islam, a religion (and an Abrahamic one at that, making the comparison even better, right?). The intent of the OP, I can say with great certainty, is not "

you, jebus! you suck and mohammed rules!!!"
The point is that all religions are equally valid (or useless, depending on your disposition), and all religions offer freaks, mutants, weirdos, and peopl who just make shit up on the spot, many of whom can be dangerous. Furthermore, if you only select one religion to actively advocate the entire decimation of based on those radicals, you're being intellectually lazy, as well as inherently contradictory (since you aren't in favor of killing all Catholics or Republicans as well).
If you can't tell the difference between a Muslim terrorist and a Muslim citizen, how can you tell the difference between a Christian terrorist (how about Eric Rudolph if the OP's cite doesn't suit your fancy, or Randall Terry?) and a Christian citizen? Can you tell the difference between a Republican terrorist (McVeigh) and a Republican citizen?
The point has nothing to do with religion, and, as you continue to focus solely on that, you're keeping the dialogue at a base level which allows you to escape unfettered without having to deal with your laziness, your hatred, and your contradictory and religiously preferential lifestyles.