People using religion as a easy explanation cause harm. I don't think you will find the place in Bible or Quoran where it says "and crash a plane unto the unbelievers so they may die in thousands". That's simply not in there. Fanatics and idiots will always find a reason to kill. If it weren't for religion, they would kill for pink cows or world peace.
Religion does cause harm, Northern Ireland, Israel, 9/11, witch burnings, Spanish Inquisition, intereference in science's development and education to name but a few.