I guess people here have mediocre knowledge of history. I blame their education system for it. What next, the reason WWI started was because one guy was shot? Haha, haha, ha... you didn't think that was the reason, right?
Money, resources and power, those are the reasons. Religion is just one tool for politicians to manipulate people. Hell, ever wondered why Martin Luther's teachings were so popular? Because people liked it? Hell no, kings just noticed a great opportunity to gain more power and money from the Catholic Church.
Crusades? Only the firstborn in the family inherited the father's property. This left the other sons with nothing. Then comes a chance to pillage and make a fortune in other land. Woohoo, answer to all your problems.
Inquisitions and witch trials were just by fanatics, which almost all groups have. Though I guess opportunists used it to get rid of their rivals.