Recent historians of the Roman and Spanish Inquisitions have shown that, although these were not nice by modern standards, they were pretty fair and decent by the standards of the times. The Roman Inquisition never got caught up in the witchcraft craze, for example. While tens of thousands of old women were burned or drowned in Protestant countries, only a few dozen were killed for witchcraft in Italy. Even in Spain, which was a lot fiercer against heresy because of the historical background of the Reconquista and the continuing Moorish threat, and somewhat out of control of the Pope, the inquisition executed relatively few people. What you think you know about it was mostly English and Dutch propaganda--what historians call "the black legend" that was used to demonize Spain.
The modernist version of history was mostly written by children of the Enlightenment, who hated the Catholic Church and, rightly or wrongly, considered Protestantism as a better candidate for liberal modernization.
No, this column is largely accurate and to the point. There are many virtues in Protestantism, but the instrumental use of Protestantism by modernists is not one of them. That leads to the National Council of Churches and all those idiot scholars in Middle Eastern Studies departments.
No argument that the crimes of the Inquisition have been exaggerated by Protestant and Enlightenment partisans. That doesn't mean they didn't happen or that they weren't crimes, or that Catholics historically were not a lot less open to freedom of religion than Protestants. Given the relative claims to authority of the two branches, it would be very surprising if they had been.
I believe Jonah also ignores the fact that the Catholic Church in its present form has been very strongly influenced by its need to compete with Protestantism. It would be a very different Church, and ours would be a very different society, if the Reformation had not occurred. Monopolies are bad, in religious settings at least as much as in commercial ones. They're bad for the monopolists as well as for those forced to use their services.
I think you're jumping to conclusions if you assume anyone who criticizes anything about the historical record of the Church must necessarily be a believer in the Black Legend.