The Protestant Reformation was truly a powerful movement in both the religious and secular spheres. It upended centuries of accepted Christian belief in the authority of the Catholic Church to teach the Christian faith and govern the faithful. This was of course taken advantage of by the political figures of the day in an effort to consolidate their own power or reduce another's power, but the real power of the Protestant Reformation was not in its political consequences; it made a much deeper change to the mindset of the cultures of the day and strongly influenced later cultures with that mindset.
Protestant thought is usually recognized by Sola Fide and Sola Scriptura (2 of 5 Solas), a general rejection of the Catholic Church, and a strong work ethic. I was brought up as a Protestant, specifically in a Bible-believing, no instruments in worship, no alcohol, and incredibly loving and generous family. There are many things I value from that upbringing, especially the example of how to live virtuously and not engage in self-indulgence. I hold fast to those, especially now that I'm a bit older and I've learned how much better it is to live life that way.
One of the things I have since discarded from that upbringing is an intuition from which the Protestant Reformation inevitably flows. Famously, the Reformation began with the 95 Theses, a collection of grievances against the corrupt practices and abuses going on among Catholics. While it started there, it certainly did not end there. Martin Luther couldn't get past the sins of his fellow Christians. He went on to later break with the Church not just in his disagreements with corrupt practices, but in fundamental ways with its ecclesiology and scriptural exegesis.
I suspect that we can all understand what drives that leap. When someone does something heinous, there is a natural inclination to distance ourselves from the sort of person they seem to be, including their beliefs. We might be more skeptical of their beliefs which we would normally agree with because we often operate on a tacit assumption that our actions guide our beliefs in a straightforward way. Thus we would view the beliefs as the cause and the heinous acts as the effect.
The arguments which rest on this intuition are plentiful and ubiquitous in debates between Catholics and Protestants as well as debates between Catholics and folks who take the atheist or agnostic positions. They typically take the following form: "The Catholic Church/Catholic person(s) performed [insert immoral act(s) here]." These arguments are usually posed as if they present a serious hurdle for believing that the Catholic Church could be correct in its teachings.
Many Catholic apologists respond to these arguments by trying to clear up factual inaccuracies and misunderstandings that tend to accrue around these arguments. It is quite understandable to want to get the facts straight, but it's not an effective counterargument. Even after removing the factual inaccuracies and the misunderstandings which grow from a tendency to impose modern values and concepts on ancient cultures inappropriately, we are still left with the cold hard fact that many Catholic Christians in positions of temporal power have made mistakes (some of them quite heinous).
Instead of side-stepping the issue, I propose that we address it head-on. The intuition is that moral failings are a good indicator that what a person or organization believes is not true, and we all know that intuition isn't true from our own life experience. Do you believe that the things you believe (at least most of them) are true? Do you ever fail in serious ways to live up to your ideals? Have we not all hurt those we love? Have we not all failed to set aside our own egos and do what we should to help them? If we are willing to believe that we can still hold true beliefs despite our numerous moral failings, then why is it so hard to believe that a group of our fellow human beings could do the same?
Most Protestant Christians rightly understand that simply practicing good morals does not entail doctrinal correctness. After all, they believe that even the most virtuous Catholics are seriously in error on matters of doctrine. Even a tree which bears good fruit may not be in possession of truth, and to the extent that we are all trees who have borne fruits both good and ill, I hope that in the same way, my Protestant brothers and sisters can also realize that sin (no matter how grievous) does not keep either their churches or the Catholic Church from having the fullness of truth.
While the topic of the moral failings of Catholics should be addressed by those who have committed wrongs by seeking forgiveness and practicing genuine repentance, those moral failings have no bearing on whether or not anyone's beliefs are true, including the teachings of the Catholic Church. The issue of whether Catholic teaching is true would have to be addressed by other means.
For more on Protestant Intuitions, see part 2 of this series here.
Note: Above is a picture of Martin Luther's edited Bible translated into German.