Give Papal States gifts all the time, and you'll be good.

I like to start being agressive towards a faction that attacks me when I have full pope-o-meter. Then it'll take many hostile actions from me before the pope threatens with excommunication. Then I manage to take, say three settlements, and I give one of them to the pope as a gift. Reputation with the pope can for example then go from 3 crosses to full bar.