I've heard this comment thrown in or argued for several times. I'd never even considered it, and I think that anyone with a grasp of history would argue against it, if for no other reason than that "all" is pretty difficult to defend.
So I started thinking of wars. The closest I can come up with may be the Crusades, and possibly the wars of Islamic expansion from centuries ago. My understanding is that most historians think that the crusades were more about reducing destruction in Europe by diverting armed and violent men to the middle east than actually fighting for religion's sake. I have to take that with a grain of salt though, because the few things I have read that were written by the Christian participants make me think that they really believed that they were "fighting for Christ." Even this being the case, I don't think religion "caused" the conflicts. I think it was used as an excuse for the conflict. Anyone that reads the New Testament objectively knows that physically initiating violence was not Jesus' way, or the object of his teachings.
The wars of the expansion of Islam can probably be seen in a similar fashion. In name they were to increase the religion/destroy the infidels, but in reality most of the teachings of Islam are peaceful.
Today's wars in Iraq, Afghanistan, and Libya can be viewed at a glance as a war between Christians and Muslims, therefore a war between religions, therefore religion caused the wars, but a view with any depth reveals that religion has nothing to do with the cause of these conflicts. At least not the West's part in them. The US went in due to terrorism, weapons of mass destruction, for oil, to promote democracy, because it's in US interests, to protect the innocent, to remove dictators, because George Bush Sr. didn't finish what he started, etc. Lots of reasons thrown around for the cause of the conflict, but is religion one of them, really? The US certainly doesn't act like it. The wars may benefit one Islamic group over another, but it doesn't benefit Christians. In other areas where Christians specifically are persecuted and killed (like Sudan), the US doesn't do anything so radical as direct military intervention.
While it may be true that Osama Bin Laden claimed religious reasons for attacking the Great Satan, 99% of muslims share a belief in Islam but don't even consider initiating violence against the US. Osama Bin Laden's violence wasn't because he was a muslim. Being a muslim allowed him a reason to express and direct his violence.
In other words, "religions don't kill people, people kill people." There are many terrorist groups that have no religious element at all to provide a reason for killing innocents. Ask any Colombian. What really upsets me is when people use this argument in an attack on religion. usually this comes from someone who's made science their religion. In World War II millions of Jews and others were killed because "science" indicated they were from inferior races.
The "science" they used was flawed and misinterpreted. Again, I would say it wasn't really science that caused these terrible events. Rather, it was people that used it as an excuse to do what they wanted to do.
It could be argued that science created the weapons that end life during every war in history. Science and religion are both tools that get used by those that hate, or desire power, to get what they want.