It is a joke on the popular response: "Is the Pope catholic?"
It refers to the Pope backing up many Catholic Priests that were convicted of the rapes of young children.
This phrase was first quoted by Eric Cartman in the South Park episode: "Medicinal Fried Chicken".
In that episode, he also made two other quotes:
"Is the Pope catholic... and making the world safe for pedophiles?"
Does a bear crap in the woods... and the does the Pope crap on the lives and dreams of 200 deaf boys?
Eric: "Does the Pope help pedophiles get away with their crimes?"