It's no surprise the Pope is the physical icon of Christianity, so he would be hated. Sure there has been issues with the Catholic Church in the past with various other groups of Christians such as the Orthodox, Lutherans, Anglicans, and so forth, but that is not the only reason why he is hated. Another factor is that the Catholic Church is the only visible Church in the entire world. You don't hear any hatred directed towards Orthodox, or Lutherans, or Anglicans, etc. etc. that's because they are not visible in the eyes of the public.
The thing that bothers most people is the fact that the Catholic Church is very secretive. This of course leads to conspiracies and scandals, but there is a reason why it's secretive because the Catholic Church believes in confidentiality (hurting the reputations of others is scandal which is in itself a sin). And confession your sins to a Bishop or Priest is done so in confidence that it will remain a secret. People don't like secrets.
And consider this the Catholic Church is very political, the Vatican City is itself a nation headed by the Pope according to Non-christians the head of all Christianity in the world. Do you know how many Kings/Queens, Emperors/Empresses, and Presidents of other nations confided with the Pope? So literally in the eyes of the world if the Pope says or does something he is representing all of Christianity in the world. It doesn't even matter if your Orthodox, or Protestant, or whatever type of Christian you call yourself.