Wteberon, you are correct when you say there were times when the Catholic Church abused its power, and labeled non-Christians as heretics. (Actually, they usually labeled them as pagans, infidels, etc. It was Christians who were a little too far from the mainstream who were labeled "heretics.")
Still, my point is that for any book to sum up the history of the Church in Europe as something to the effect of "The Catholic Church persecuted anyone who didn't scrape before their omnipotence," is inaccurate and over-simplified. It ignores Eastern Europe entirely. It denies the many minority groups who were not just local, but spread across Europe and who endured the peaks and troughs of persecution, such as Franciscans and , say, Jews. It denies the fact that ecclesiastical power rose and fell. While it was sometimes abused, sometimes it acted as a check on the power of monarchies in the abuse of their power, and visa versa.
Persecution was wrong and evil, but it was not constant and unabated. There is more to Europe's religious history than that.