Typically, religion tends to act less as the cause of conflict, than as a justification, or as a force-multiplier. Complex conflicts over resources or nuanced political entanglements can be - for purposes of emotional manipulation of the population - distilled down to a single, shared identity marker, and exploited to mobilize an otherwise uninvested population.
These even applies to ostensibly _explicitly_ religious conflicts: the First Crusade was actually prompted more by migration, than religion.