Examples of people doing bad things in the name of the Bible is not evidence of anything against the Bible.
Christianity, and catholicism more specifically, are more than just the Bible itself.
Religious teachings evolve over time based off of new reinterpretations of old passages, teachings from influential leaders, folk traditions that spring up, etc. Those are all part of the religion, too.
For example, most Christians would say that the serpent in the garden of eden is Satan. Yet Genesis doesn’t say anything about that, and the New Testament doesn’t explicitly say it either. Mostly, it’s a folk tradition some people found a couple verses you could squint at to support it.
And particularly in the case of Catholicism, there’s a world of difference between a pope issuing an official bull, and your neighbor being a catholic who happens to be a shitty person. There’s a huge difference between a random person teaching to be nice to your neighbor but shitty to outsiders, and for St Jerome to do that.