Nah, religion's cool. It's zealotry that fucks everything up. When you're raving and spitting, and have a hard on for whatever subject you're pressing, you're guaranteed to over do it. When you're creating something, or a builder of something, that zealous nature will push you into production. When you're zealous over how people should act and think, in a theocracy that uses religion as a tempering and control mechanism, you're going to become thought police guaranteed.
Overzealousness and theocracy are the problems. Not to mention general ignorance about the religion and the foundations of it and the basis behind it. Religion is still just a tool. But people would rather use it as a murder weapon to repair their hurt sensibilities than to actually use it for self improvement.
(ironically enough, Hitch was thought by many of his peers to be an overzealous anti-religionist)