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Maher repeats this same argument that you hear all the time in these circles; other similar anti-religious comedians, Hicks, Carlin, repeated it. They say that all the worst wars, or most of them, are owed to religion, or religious hatred. That's bogus. I'm an atheist, and one that will tell religious folks what I think of their dumb ideas, but this 'wars of religion' thing is just another dumb meme.
Take recent history for example. Were the Vietnam or Korean wars about religion? What about the Chinese Civil War? The Japanese invasion of China? What about the Russian Civil War? What about World Wars 1 and 2? The Franco-Prussian War? The Opium Wars? The War of the Spanish Succession? The 100 Years War? The American Revolution? The American Civil War? The Manchu Invasion of China? The Mongol Conquests? The Ottoman Conquests? Wars of the Chinese, Roman, Greek, Persian, and other Empires? None of them were about religion. Most of them were about political, or ethnic conflicts, or about gaining territory. Is that a reason to argue against ethnicity, or policy? If anything, truly religious wars are an exception to the rule.
Saying religion is dumb is fine; just don't employ equally dumb arguments in doing so...