If I'm not mistaken PayPal just chooses not to allow firearms transactions via their service, which I totally understand in this lawsuit happy environment that we live in these days. They don't want to be held liable for anything. Even the gun shop that the kid from VT purchase his guns from got sued in civil court. They don't donate to any antis like Brady or anything, they just don't want to get sued. Sure they are owned by eBay but they aren't big donors either. Correct me if I'm wrong.

I came across this as well, they explain why they continue to use PayPal even though they are a gun organization:
New Jersey Coalition for Self Defense