***D. Alleged and Real Corruption
Non-Catholics point to many examples of corruption and mistreatment in both the modern and past Catholic Church and see this as representative of a poor relationship with God. You Catholics have your Saints, we Protestants have Martyrs – and I’m sorry to say this, but a rather lot of them were executed by Catholics. These events are not commonly discussed on these forums for obvious reasons, but there were many atrocities. Unfortunately, the issue is not really quite so black and white. Protestants also martyred and mistreated Catholics. Atrocities were committed on both sides and there is corruption in both organizations. Unfortunately, recent crimes committed by Catholic clergy has done nothing to assuage these beliefs, but only made the conflict greater. Nonetheless, I think this criticism is invalid and cannot be applied to the majority of Catholics.
E. Claims of Infallibility
Non-Catholic church’s balk at Church claims of infallibility, for obvious reasons. Some Protestants that this is heretical, stating that only God is truly infallible. All man’s works are fallible and incomplete and the Catholic Church is no exception. For the most part, this is based on misinterpretation of Catholic claims (at least, modern Catholic claims; I have no clue where more traditional Catholics would stand). Papal infallibility, as many have told me, does not apply to everything the Pope says and certainly not to everything the Priests say. Regardless, the way Catholics phrase often leads to unfortunate misunderstandings.
F. Baptismal Teaching
Many Protestants (well, it depends on who you ask, some denominations are different, obviously)

, believe that baptism does not save and has no power to do so. Some view it as merely symbolic, others view it as spiritual, but not saving. Some reject its usage on infants, believing it should only be used on those who have accepted Christ as their savior. [From personal experience, my church honestly did not care what you thought. Though they rejected the concept that baptism saves, they allowed infant baptism as a sign of the church and a promise of God’s protection, but also baptized adults and teens when they had passed our inquirers class, if that was their preference.]
Regardless, many reject the concept that you are save by baptism. Physical baptism has nothing to do with salvation in their opinion. It is the power of spiritual baptism that saves and you don’t need water to do this (though obviously, no Christian I know of objects to Baptism by water). This is where I would disagree most strongly with Catholics, particularly because of some of the things I have read on this forum, where some people honestly seem to believe or imply that baptism by water is essential for salvation. I hold that they are very wrong and that this belief is harmful, particularly because it leads some to believe that those who leave the church but don’t commit any mortal sins are still saved. Ultimately, however, I don’t think this is the view of all Catholics and I don’t think that that it is worthy of being called heresy, particularly since Protestants are also of this view.
G. Oddities
There are other reasons for objection, including Transubstantiation, all the gilt and statues in your churches, and some biblical prophecies about Babylon. Most of the ones in this category are just too crazy/misunderstood to deserve a mention.
NOTE: I am NOT trying to attack Catholics or defend Protestants. Please do not get into an argument with me over our doctrinal differences. I am merely trying to explain why some Protestants (in my opinion, mistakenly and due to dis-information) believe what they believe about the Catholic church. If I have misrepresented your Church’s doctrinal statements (I’m sure in all of this you would find something at least poorly worded) please supply a correction.
Sincerely yours in Christ,
FractalFire