Protestantism, by its very nature, is restorationist. It believes that historical chrstianity is a "great apostasy" and that "true chrstianity" was "restored" at whatever date their various churches were founded. "Whore of Babylon" is a way of expressing this opposition to the historical churches. What are they supposed to do? Say "there's nothing wrong with historical chrstianity but let's start a brand new church for no reason whatsoever?"
Catholics likewise believe that Protestants are heretics, rebels, ignorant of history, etc. I notice this is never considered "bigotry," however.
FR Catholics need to stop playing "oppressed left wing urban minority" by constantly shouting "bigot!"