I'm pretty sure I said it was ONE OF the biggest causes. Which I think it has been.
It really has not. Take out the Crusades, the Muslim Conquests and the French Wars of Religion and you're already running low on wars started by or religion being a factor in causing it.
The expansion of empires, civil wars, independence and fighting over resources and trade routes are much much more common in history for the cause of armed conflicts.
Religious war still goes on today in the form of terrorism.
It's really a combination of things. Yes in the fact that people are doing it because they are Muslim, no in the fact they are not doing it simply because they are against non-Muslims. The terrorist acts originate due to fighting over land, land Israel now occupies, which they believe belongs to them and the Arabs believe it belongs to them. Further escalation in terrorism occurred due to the Afghan and Iraq wars. America has been an ally of Israel for quite some time and this is where the bad blood comes from, not because they are not Muslim. Due to the Palestine problem, both invasions, most of the Muslim world (Which see each others as family anyway) feel as if there is some serious problems against just them.
Take out this land problem and you'd find fundings cut off for most of these terrorist organizations almost instantly, of course for that to happen it mean Israel would cease to exist, which will not happen, so this will undoubtly continue for the ages.
These acts of terrorism are much more complicated then simply just "We must kill the non-believers!" most of it originates from the problems between Palestine and Israel and foreign policy of other countries. Most are funded by rich Arab who want their land back and people being cohaxed into it, as I said, a combination of things.
Anyway, what about the Tamil Tigers? Or former problems like the Japanese Red Army and IRA? Or Chechnyan Separatists still in action? There are many many other terrorist organizations out there which have nothing to do with religion.