Crafty a species as humans are, we're still posessive, territorial apes easily driven & controlled by fear. While a lot of things can make us afraid or angry enough to trigger violence (competition over territory, mates, resources; threat of invasion or attack - real or not), religion has the ability to raise the level of fear to extremes. Raise a child to believe it'll burn in hell for doing the wrong thing and, understandably, anything the resulting adult has to do to avoid such torment is justifiable. Certainly, bribing the same person with promises of eternal life, heavenly reward and sitting at a god's table is also a potent motivator, but the fear of just missing out on such rewards is arguably as potent as a fear of eternal punishment.
Not all wars or genocides or atrocities have been religiously motivated and I'm unsure what the proportions are when it comes to comparing religious conflicts with those of a more secular nature. However, those wars with religious motivations, hidden or blatant, often display the most depraved forms of violence and torture. We're probably all familiar with the Crusades, launched by European kings to wrest control of the holy land of Palestine from the infidel Muslims, resulting in hideous brutalities and massacres. So too with the conflict in Ireland which felt like it would last forever and claimed the lives of many innocent people (Omagh will stick in my mind forever) - a crystal-clear demonstration that even people of the same religion can hate one another with a burning passion that eclipses all reasonable thought. Hitler's invasion of Poland may not have had religious roots, but his loathing of Jews definitely did. Though a Catholic by birth (a faith he never renounced; he was also never excommunicated by the Vatican) he drew venomous inspiration from Protestant Martin Luther's vicious rants against Jews. Though it could be argued he wasn't even a faithful man (despite his pseudo-Norse god worship strengthened by old myths and the Wagnerian operas based on them, mashed up with Neitchze's ubermensch concept), he at the very least knew how to use it to motivate and mobilise his supporters and followers. The SS, after all, had "Gott mit uns" (God is with us) on their belt-buckles.
Add to this the examples of Israel/Palestine (ruthless territorial expansion based on belief of cultural superiority, combatted with suicidal martyr attacks); the Inquisition, which featured tortures and privations that would make the Abu Ghraib torture squads look positively tame (though the Abu Ghraib criminals use many of the same tactics); the 9/11 attacks, seemingly carried out by Islamic martyrs; Bush's response to 9/11, alleged to be at least partially divinely motivated - though I suspect his own decision-making capabilities had very little to do with actually kicking it off, considering his considerable difficulty even in deciding which word to say next.
There are more examples of religiously motivated conflict of course, and many examples of purely secular human conflict. Even if all religions were declared officially false and bogus and outlawed tomorrow, people would always desire to kill each other. There would still be conflicts over ideas as well as physical things like territory. There would be still dogmatic beliefs, immune to reason or logic, which elevate a single idea or goal above all else in a very fundamentalist way and there would still be ruthless dogmatists ready to pursue those ideas without regard to humanity or reality.
Stalin, Pol Pot and others are often used by the faithful as bats to beat atheists with, as if to say "religion kills millions but so does a lack of it!" This is a classic strawman attack though - it wasn't their professed lack of belief in gods that drove them to put millions to death and decimate their countries, it was their dogmatic, unfounded belief (their "faith") in their narrow ideals and singular vision (and unquenchable thirst for sheer power) that drove them beyond reason and into fundamentalist dogma which eclipsed all else. Even if you remove god-belief from an equation, any unfounded belief, any faith, held strongly enough and made immune to reasonable, logical challenge can lead to unspeakable horrors - and quite often, in an Orwellian reversal, under the flag of utopianism.
So, while it's true that religion has been the root cause of many unthinkable injustices, murders and genocides, what really needs to be addressed are the issues of faith: the belief in something with no foundation or reason to do so; and dogma: the solid, blinkered adherence to that belief in the face of contradictory evidence. Whether you believe the creator of the universe wants you to destroy infidels to hasten a new age or Armageddon, or you believe you yourself (or your leader) to be the ultimate power on earth, your blind, unquestioning faith in either of those things is the most dangerous weapon in your arsenal.