They weren't persecuted for BEING Catholic and holding to the Catholic Faith.
They were tried for heresy. Now, whether they should have been burned at the stake----we can agree that such was not a good idea. At the same time, making a statement like that is easy in a modern culture where Church and state are not intertwined. Heresy was seen as treason--hence--why they took such a strong armed approach in combating heresy.
The point, however, is that Luther, Waldo, Hus and Wycliffe weren't persecuted by the Church; they were tried for heresy.
Do you mean to suggest that God's Church should allow falsehood and untruth to fester unchecked? If so, then, does that mean that I could be a minister in your Church and deny Sola Scriptura or Sola Fide and get away with it?