I have meet many Catholics who are shocked to learn that many Protestants hold their Church suspect and don't trust the word from Rome. Many modern Catholics don't understand why this is. One reason is because people have long memories, that often lasts for many generations, when wrongs are done to them.
The Catholics do have Martyrs from the Reformation era, but for every one Catholic martyr There were many times more Protestant martyrs who died horrible deaths with the nod of the Roman See. For every Sir Thomas More (who had Protestants in England killed for their Faith) there were many more Protestant Martyr's. I think of men like William Tyndale, Hugh Latimer, Nicholas Ridley, John Hooper, John Bradford, Thomas Cranmer etc....
Roman Catholics can not pretend that the Church at Rome did not encourage that the sword, the stake and the Inquisition be used to suppress and destroy those that had broken with Rome. To say "That was then this is now" is not enough, especially if you claim to be the "true Church" and some amount of infallibility, as Rome does.
I want to see reconciliation in what is left of Christendom, but I am not foolish enough to think that will be easy. It want be, but we need to work for it and we need to be HONEST (a Christian virtue) when dealing with each other.
Some years back A Roman Catholic was offended when reading a copy of the Westminster Confession, because of some of the harsh things said about The Roman Catholic Church in it. My response was, "Have you read what the Catholics said about Protestants in the canons from the Council of Trent?"
In the religious disputes that racked Christendom after the Luther broke with Rome, there was wrong committed on all sides, but Rome was bigger and hit harder than any of its Protestant rivals were able to do. These things need to be dealt with and not simply dismissed as being unimportant because it was long ago. Wounds can last for millennia if there is no attempt at healing.