Protestants disagree with the Roman Catholic Church because it claims to be infallible, and we all know only Martin Luther was infallible.
Protestants think the Catholics teach the precepts of men instead of the word of God, they don't follow dead tradition, they follow Spurgeon and Wesley's tradition.
The Catholic church says that they only believe in the initial doctrines of the disciples...but that Papal authority and the Papacy developed...so by following their original teachings you have to reject the Pope.
Protestants claim that salvation comes from faith not works, and then criticizes Catholics on the basis of the lives that they live.
Catholics use the bible to try to disprove Sola Scriptura.