Though the original reasons for the disagreements against the Catholic church are many and varied, you could also look at which ones have become the pivotal points that separate Protestant and Catholic churches today, and cite these as what ultimately arose as the "most important."
I think first, and foremost, Protestants disagree with both the power and the authority of the Pope. Catholics, simply put, consider the pope to be the most important figure in the church and as far as authority goes, he is the closest human to the heart of Christ (essentially). Protestants basically believe that all of humans have equal opportunity and standing in the eyes of God, and everyone is called to the same accountability for their actions. Humans, in other words, cannot pardon other humans from sin. All are equally judged by God himself and all have the same opportunity for communication with God the Father through the death of Jesus Christ on the cross.
Second, Protestants disagree with the transubstantiation of the bread and wine at the Eucharist actually becoming the body and blood of Christ. Protestants practice communion in a purely symbolic way, as a part of worship that "remembers" and celebrates Jesus's death and resurrection. Catholics believe that with the blessing of the bread and wine, the two objects become holy and are actual pieces of Christ's body and blood. Therefore, the Eucharist is more than symbolic, and also more exclusive. Not just anyone can partake in the Catholic sacrament of communion.
And finally, I think the Catholic revering of Mary (and the saints) continues to be a point of contention with Protestants. Protestants do not believe Mary remained a virgin forever. Most Protestant denominations also do not pray to Mary or other saints.