The problem isn't with the Pope's religious beliefs - that is NOT the reason they are calling for his arrest. The problem has to do with the use of his status as a religious leader to not arrest him. If the leader of pretty much any other organization had attempted to cover up sexual abuse of minors in his or her organization, you can damn well bet that he or she would be arrested. If the CEO of a major corporation covered up sexual abuse by his employees, he'd be arrested and the board of directors would remove him from his position. I'm pretty sure even the President of the United States would at least be impeached for covering up such an action. So why not the Pope? What makes him so special?
And hey, if you think that the evidence of the Pope's involvement in the cover-up scandal (and there is at least some) isn't enough for him to be arrested over, much less convicted, then you shouldn't have any reason to worry about it.
There is no proof of the pope committing any crimes.
And of course this is motivated by religion. Atheists seethe with hatred at the pope and any other religious figures who defy their world view.