Two possibilities...

[Chad32]

Whichever book, chapter, and verse the church used to justify what they did, because Jesus wasn't around to set them straight when they screwed up. All across the bible, it sets up an us vs them mentality. You're either with Jesus, or you're not. And don't ask me to quote which book, chapter, and verse that's in, because it's one of the major themes of the whole thing. The jews aren't with Jesus, because he didn't fulfill their guidelines for the messiah, so they became the enemies of christians.

That's the thing, they didn't. They used the authority of Jesus supposedly passed on to peter and every other 'pope' from Him to the one who decided to wage war against the muslims or jews or whom ever. The problem with that? The word in which Jesus used to identify 'peter' is not one of authority. Jesus was actually being a little insulting to peter/petros (translated: loose gravel/unsure footing/small stone) when He told Him of the 'rock'/petra in which He would build His church.

Besides all of that, Peter did not start the R/C Church, Peter did not have a big gentile ministry, and nothing ever written places him in Rome. it was Paul who started the church at rome, and nothing else ever written by Peter or Paul hinted at Apostolic powers/Authority being passed down.
So again the authority given to persecute jews or anyone else was not biblical in orgin, it was a mandate from a religious leader. Such mandates do not bind God into accepting or identifying such men or their followers as 'Christians' just because they claim to be. Again that would be no different than me calling myself an Atheist and then proclaiming that God is alive and well.

Just because I give myself a title does not mean I belong to that group. Again with Christianity their are established guidelines, and when you break those guide line you are no longer worshiping the god of the bible. That however does not mean you are not a devoutly religious person. It just means your religion does not follow the God of the bible.

Originally catholicism WAS christianity, so if they got it so wrong so early in their ministry, what hope do we have of figuring out the right way to do it? The best we have is the bible, which was in the hands of people that got it wrong from pretty much day one. Whatever christianity is now, it isn't what any historical Jesus wanted. Might as well throw the whole thing out.