I'm pretty sure it's firmly rooted in the history of Christians flat out torturing and murdering people who were not Christians and even torturing and murdering other Christians for not being the correct type of Christian.
Alot of people are still pretty upset about that.
Yeah there is a lot of shitty history.
It is not really unique to Christianity though. It is not even unique to religion. Pretty much all of history involves groups of people being shitty to other groups of people. It's happened with Christianity, Judaism, Islam, pagan religions, and even places without any major religion at all (most of the history of China for example).
I think ultimately the bad stuff in history is mostly the fault of humans being shitty and greedy.