It's probably true that most people have been killed in the name of religion, but that's not the real reason they were killed. Religion was just the cover story to motivate people to go out and kill. The really underlying cause of all of these deaths is the political power of the state.
It's true that there are violent and deadly religions ( such as Kali's thugee devotees, or child sacrifice to the gods ), but religion isn't necessarily the cause of war and violence. Power and politics, almost by definition, are. You find plenty of examples of totally peaceful, pacifist religions ( just as a few examples, the Mennonite and Amish churches ). The early Christians were pacifist to the point of being regularly martyred. Then, when Roman Christians started gaining positions of power in the Roman government, and Christianity eventually became the official state religion, that's when you see Christians persecuting others. It wasn't religion or Christianity that caused the violence -- the violence only came about after power entered the picture. On the other hand, you never find a peaceful government or country. It's a contradiction in terms. The state ultimately enforces its rule through violent coercion. So, religions may or may not be violent; but governments, by definition, are. In the case of Islam, Mohammed was also a political leader ( he was basically a tribal chief, responsible for the defense of his tribe ) as well as a prophet.
So yes, people have been killed in the name of religion, a lot. But I argue that more people have actually been killed by governments.
But, some might ask, if religion is a cover story that governments use to kill people, why not go ahead and suppress religion, to prevent governments from using this powerful cover story? It's because you're not really addressing the real cause of the violence. If you take away one cover story -- a religion -- government will simply come up with another cover story -- another religion, or a mystical super-state, like Hitler's 3rd Reich, or Stalin's communist revolution.
If you're serious about addressing war and violence, religion is not the culprit. If it's just another reason to bash religion, well go ahead; religious people certainly deserve the criticism of going along with violent, evil state powers.