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You are right, many wars are not overtly about religion. The priests/preachers on both sides just bless the soldiers and tell them God is on their side.
However, some wars are specifically or at least ideologically religious. I think war is mostly an economic issue, and NOT a philisophic ones. So the Crusades were wars against Islam, but perhaps to pick up some booty and strengthen the Catholic Church. Much of the recent fighting in the 'former' Yugoslavia was nationalist, but also religoius-based nationalism. We can't, of course, forget Northern Ireland, where religions are a stand-in for nationalism and imperialism.
The 30 Years War was one of Protestants against Catholics. Fascists in Eastern Europe under the Nazis were mostly Catholics - and of course, what do you think right-wing Catholics thought of Jews in those days? The war against the Soviet Union in Afghanistan was of Muslims against secularists. Within Iraq right now, the fight is between varieties of Muslim, with another potential fight versus Kurds, who are Sunni, but also Shiite and Zoroasterism, Bahai, etc. I.E. national identity is many times glued together with religious identity, and as a result, religion and nationalism are one - a dangerous combination by the way.
What Mahr is referring to now is the jihadist views of part of the Islamic world, and the Christian-soldier views of part of the U.S. Christians - including Bush and Palin. We certainly know the fundamentalist Jews in Israel want war against the Palestinians, and visa versa - and this way of looking at the world has now been spread by the Bush family. I.E. religion right now is becoming MORE of an issue... in case you missed that. Which is why atheism has become more aggressive in dealing with this resurgence.