One of the big causes of the Thirty Years War in Germany (1618-1648) was the conflict between Protestant and Catholic rulers.
The French Wars of Religion (1562-1598) was based on the same Reformation conflict.
No war has just one root cause. There are always preeminent social, economic, and political elements to any armed conflict.
When people say the Crusades were based on religion, they forget the vast political and social causes of the conflict.