The same reason most Muslims have to make up for the insanity of a few. Or any other group for that matter. It only takes a few bad apples to spoil the bunch. Cliche I know, but still true.
Because let's be honest, it's not just a few that are the problem. Historically speaking, i can't think of a single other institution responsible for more deaths, torture, or forced conversions than Christianity. Now a days organized religion serves as the last socially acceptable medium for bigotry and institutionally sanctioned hate. I mean it's in your book, kill everyone who's not like you.