Bad things happen outside the name of christianity also. I'm not saying the crusades and such were right. I think it's unfortunate that people look at the crusades and such and therefore decide that christianity or another organized religion is fundamentally flawed. The bottom line is that those types of things aren't accurate representations of what the religion is all about. You can go out daily and see religious people (and non religious people at that) doing things that people would definately approve of, but christians are still remembered for things that happened forever ago. A similar, although possibly slightly askew, comparison would be saying that America is messed up because it dropped an A-bomb. We killed sooo many people. Now I know there are arguments like "it ended the war," and "Imagine the amount of lives that would've been lost had the war continued for 5 years." I'm not here to decide if the a-bomb was right, that's not my point. My point is that there were probably similar "excuses" like that for the crusades and such, and wheter right or wrong, they don't represent the group or beliefs of the whole.
*I just focused on the crusades for ease of typing. I'm not some kind of crusades defender. Heck, I don't really know much about them at all.