Because at some point, someone feels threatened by a different person's belief system- maybe because they're not 100% certain of their own, deep down inside, or if they're misunderstanding it, or afraid it can cause harm to themselves or loved ones- so they say something mean. The other party, seeing that this was unjustified in one way or another, lashes back. Rinse and repeat.
It is human nature to define "other" and then to try to get rid of it, because "other" is a threat to "me" or "us."
Oh, and if it's not that someone's feeling threatened in a scenario as above, it's that they're a douchebag stirring up trouble, which is also probably because they're feeling threatened or like they don't have any control or why didn't I go into psychology...
hem...