Well first off you are playing the HRE..... Pope hates you unless you bribe him constantly. If you don't listen to the pope you get excommunicated doesn't do anything big just a little bit more unrest in your cities. Three ways you can fix that are Faction Leader Dying, Pope Dying , or Bribing the hope back into his good graces.

Your post is a little vague so I don't know what else you would like me to say