Throughout history, some truly gut-wrenching acts have been performed in the name of religion. The Crusades, 9-11, and the Inquisition all stand out as (in)famous examples of extremism and atrocities that were justified using religion. These acts were certainly carried out in the name of religious beliefs and leaders, but whether the non-existence of religion could have prevented them is debatable even among atheists with no love of religion or spiritual beliefs.
Richard Dawkins and Christopher Hitchens, both writers placed by the media in the "New Atheism" movement, certainly see these atrocities as the product almost entirely of religious thought. Hitchens went so far as to subtitle his book "god is not great" (he purposefully wrote the word god with a lowercase g) as "How Religion Poisons Everything". He has gone on to defend this statement in public debates, stating that religions of all kinds, whether the Dharmic religions of Asia or the Abrahamic religions of the Middle East and West or even the animist religions of other regions of the world ultimately inspire only bad behavior among their followers and lead them to commit religious atrocities against non-believers.
Other atheist thinkers are not so sure. Although Daniel Dennett is also considered a member of the "New Atheism" movement, in interviews he has drawn a distinction between negative and neutral religious thought, implying that religion does not necessarily cause violent behavior in its followers.
The creators of the hit cartoon series South Park, Trey Parker and Matt Stone, are certainly no friends to organized religion, having at this point skewered almost every major religion in America in addition to many religious figures such as Muhammed, Jesus, and the Pope. However, they wrote and produced an episode parodying "New Atheism" where they showed a world without religion in which the equivalents of crusades and jihads were being waged by rival atheist organizations. The point of the episode was to show that writers like Hitchens and Dawkins were wrong, and that without religion humans would find new pretexts to fight. According to Parker and Stone, religious atrocities are really human atrocities, with religious extremism being simply the most convenient justification for human violence.
It's certainly true that humans can be very violent, even in the absence of organized religion. In his book "Guns, Germs, and Steel" Jared Diamond describes how tribal societies suffer large amounts of violence, as there exists no authority to reign in conflicts between people. According to him, religion grew as a way of calming tribal violence, giving people a reason not to kill people they were not related to and justifying the authority of tribal chiefs to maintain peace by any means necessary.
Given this history of violence, one must sadly conclude that violence is an endemic condition in humans, and even without religious motivation humans would find many justifications to hurt each-other. Certainly, some massive atrocities were not done entirely at the urging of religious leaders and scriptures. While the pogroms and discrimination against European Jews were caused by religious differences throughout most of history, the Nazis murdered those they considered ethnic Jews even if these people had converted to Christianity. And in the case of the Rwandan genocide, while some religious leaders helped lead the murder of ethnic Tutsis, others sheltered Tutsis and the genocide itself was undeniably inspired by ethnic differences that had nothing to do with religion.
While religion has unarguably inspired the extremism and atrocities such as Al-Qaida and 9-11, ultimately many factors cause actions as complex as genocide and war. Religion does not always inspire atrocities, and what we may call religious atrocities are sometimes caused by more than just religion. To lay all the blame for human violence at the feet of religion is ultimately an answer that is too simplistic and does not consider all the facts. Skeptics should therefore reject this claim, and base their criticism of religion and religious organizations on better arguments.