The problem that protestant christians have with catholics is simple. The large majority of the unique Catholic dogma is simply unscriptural. The bible never gives the catholic church, much less the pope, any authority. Scripture is the basis of the christian faith (ideally) and the greater part of how the catholic church sets itself apart is unscriptural.
Justification
The first point of contention is the issue of justification. Justification cannot be earned from a scriptural point of view. As Paul says in Galatians, "I do not nullify the grace of God; for if righteousness comes through the Law, then Christ died needlessly" (2:21). We do not earn grace by trying to earn grace as the catholic church is wont to suggest. The catholic suggestion that we are merited grace by baptism is absurd. We can never merit grace. Merited grace is an oxymoron. Something being merited implies it is owed to us. Do you really want to suggest that God could owe you salvation for anything you could do? This teaching says we should not have peace in christ, instead of what Romans says: "Therefore being justified by faith, we have peace with God through our Lord Jesus Christ" (5:1)
Grace is a gift, not a right. You can never do enough to atone for your sins. Christ is the only way to heaven - not baptism, not indulgences, not the sacraments of the catholic church.
"But we are all as an unclean thing, and all our righteousnesses are as filthy rags" (Isa. 64:6)
Catholic doctrine, here, opposes scripture.
I don't trust in myself for salvation, I trust in Christ.
Transubstantiation
All I'm going to say here is that Jesus had a habit of using spiritual language. If we are to take his words "this is my blood" and "this is my body" literally, then so too must we take at face value his statements that he is also a vine, and he's made from bread. The last supper was also an event before the crucifixion, meaning that the sacrament is a symbol of... the last supper. How can the eucharist be representative of the crucifixion when it hadn't happened yet? Was the communion taken at the last supper also transubstantiated into his sacrficial body that hadn't been sacrificed yet?
What about the hypostatic union? If the flesh of Jesus was human flesh, how does is it magically teleported into the stomachs of millions of people everywhere, constantly? Jesus didn't defy the nature of flesh. This is in direct opposition to the humanity of Christ. Jesus cannot be present physically all over the world at once during mass, because the physical body of Jesus is a human body. The body of Christ, by nature of humanity, cannot be omnipresent.
Nowhere in scripture is it even implied that we must continually sacrifice Christ for salvation. Only one sacrifice was necessary. There is no biblical foundation for transubstantiation.
Indulgences
Absolutely counter Biblical, and a bit rediculous to boot. This process probably started as a method of exerting control during the peak of the catholic church, by forcing church members to rely on the church. I'm not going to defend this position, since it's a presumption on my part. Baseless, and dangerous. Indulgences are also worthless in the greater scheme of things, as the teaching of catholic purgatory is also unbiblical. We cannot cleanse ourselves of our sins, and neither can the church.
Indulgences cheapen the sacrifice of Christ.
Mary
Mary was great, yes. Mary was the most blessed of woman, yes. Mary was the mother of Jesus, fine.
Basically everything else is unbiblical, and is NOT even part of Catholic tradition! The immaculate conception originated in the mid-1800's, and the doctrine of the assumption of Mary is only 57 years old. The early church in Rome had no such veneration of Mary.
You may deny it, but Catholicism does teach to pray to Mary, the supposed mother of prayers. Now, as you said, these prayers are asking for her to mediate your salvation, but you are praying to her nonetheless. The Catholic church has, in fact, encouraged her worship (though did not teach it, itself), saying that she would lead people worshiping her to Christ. Mary is not the model of virtue, Jesus is.
Mary being blessed is not a justification to call her the queen of angels. Such titles and merits are clear inventions of the catholic church. The book of First Timothy clearly states that Christ is the only mediator between God and man (2:5). You can ask Mary to do it, but she can't - sorry.
Did Mary remain a virgin? No, she did not. It is mentioned in several verses that Jesus had siblings.
"Is not this the carpenters son? Is not His mother called Mary, and His brothers, James and Joseph and Simon and Judas?" (Mat. 13:55)
"Behold, Your mother and Your brothers are standing outside seeking to speak to You" (Mat. 12:47)
The list goes on. While it may be true that the words brother and sister used can mean cousin, however this is entirely dependant on context. The context, in nearly every case, it that of immediate family. His father, his mother, and his brothers. To interject "cousins" into this passage, when it is in clear opposition to context, is quite a leap. If the carpenter is Joseph, and Mary is his mother, Mary, why would it ever be appropriate to assume or even suggest that when it says brothers, it means cousins? Jesus also on more than one occasion directly identifies with the Messianic Psalm, Psalm 69. This Psalm that he identifies himself with states that the Messiah's mother has other sons. If you wish to further suggest that "Mother's sons" means cousins, then I must not grasp familial relations as well as I had thought.
After Jesus was born, Mary had sex with Joseph and had more children. The only thing in opposition to this is a Catholic doctrine that is less than 200 years old.
The only - yes, only - support for the sinlessness of Mary is the passage where Gabriel describes her as being "full of grace." This is taken to mean she was born without sin, never sinned, never had sex, and was assumed into heaven.
But, Acts 6:8 says that Stephan was full of grace as well, and he was a sinner... I guess the Bible must be wrong again!
Nevertheless, Gabriel addressing Mary as "full of Grace" is unique to the latin vulgate (The latine vulgate is a Greek-Latin translation of the bible from the 14th century, from which the roman catholic church derived their doctrine), which was a bit short of a being a perfect translation in this case. The Latin vulgate is the ONLY original-text translation I know of that refers to Mary as "full of grace". This is a mistranslation! Nearly every translation of the Bible now (which, I hope we can agree, are translated from earliest possible original-language texts) do NOT say "Hail, Mary, full of grace" in Luke 1:28. "Highly favored" and "greatly blessed" are more accurate translations. The Greek text says "kexaritomena" which means "highly favored" or "accepted". "Full of Grace" is "plaras karitos" in Greek. The assumption, virginity, and immaculate conception of Mary are based on a poor 400 year old translation which was wrong.
(Please note that modern Bible are, as I said, translated and corroborated by enormous groups of language experts, supported by tens of thousands of agreeing texts, and based on the earliest possible original language material, not translated and retranslated as some like to suggest. The Latin vulgate, however, was translated by a single man, and was less accurate. The modern translations of the Bible weren't based on the Latin Vulgate)
Papacy
Even the Papacy is based on poor exploration of the scripture. The Greek of Mathew 16:18, which is the basis of the Papacy, shows that Jesus was referring to HIMSELF as the rock upon which the church would be built, not Peter. Additionally, Peter was hardly a rock. Remember when he tried to walk on water? Peter's faith was far short of being immovable. Jesus called Peter "petros", and then said he would be his church on the "petra." Petros is always distringuished from Petra. Petros is used to refer to a small stone, and Petra is used to refer to an immovable mass of stone.
Matt. 16:18, "And I also say to you that you are Peter (petros), and upon this rock (petra) I will build My church; and the gates of Hades shall not overpower it."
Peter is the stone (petros), Jesus is the rock (petra). So, if the church was not built in Peter, but on Christ, then what is the significance of the papacy?
No, seriously, what?
"For no man can lay a foundation other than the one which is laid, which is Jesus Christ," (1 Cor. 3:11).
Popes are corruptable and fallible, just like anyone else. Only God is infallible.
So you see, the problem that protestants have is that Catholics refer to the Catholic church for the ultimate authority, while protestants appeal to the scripture. The catholic sacred tradition is often at complete odds with the scriptures that they claim affirm it. The Catholic church venerates individuals dangerously, and follows a man who has no scriptural authority.
(Please note as I have approached this topic that I believe that many Catholics are, in fact, saved - those that rely only on perfect attonement brought by the sacrifice of Christ. To deny the completeness of his sacrifice is to, I believe, deny salvation. Also note that while the apocrypha is part of this discussion, I won't approach it as I don't know enough to speak with any confidance, and it's far too complicated for me.)
Cheers.)