One of the worst examples of abuses perpetrated by anti-theism: Stalin slaughtering 20 million. The worst example that atheists can think of for the Catholic Church: Galileo … a man who had disagreements with the Church hierarchy (for disciplinary, not scientific reasons) but was still nonetheless deeply Catholic… a man who died a peaceful/natural death and whose daughter became a nun!
Atheists always seem to trumpet the ‘Scientific Revolution’ as a moment in which scientific rationality supposedly began to turn the tide against “religious superstition.” What they fail to realize is that all of the major thinkers of the ‘Scientific Revolution’ were theists. Yes, a few of them (such as Newton), had deistic tendencies … but the vast majority of them were orthodox Catholics (e.g. Copernicus and Pascal) or at least Protestants (e.g. Kepler described himself as “a priest of the most High God”).
The fact of the matter is that modern Western science has its most fundamental roots in the Catholic Church. I love it when atheists ask: “How can you reconcile your Catholic beliefs with the Big Bang Theory?” only to learn that the Big Bang Theory was in fact developed by a Catholic Priest! (Fr Lemaitre) The father of modern genetics - Gregor Mendel - was a Silesian monk. Modern optics has its roots in a work called the Opus Maius, written in 1297 by a Franciscan. The list goes on and on…
And for the record, Galileo was never tortured. Did individuals within the church make serious mistakes with regard to how Galileo was treated? Yes - but the Church was and is full of both saints and sinners. And Galileo was not put under house arrest because the Catholic Church was “against science” … it was due to disciplinary disagreements concerning the ways in which Galileo presented his arguments and to unfortunate intra-Church rivalries. The Jesuits (and Pope Urban VIII himself!), for example, strongly supported Galileo’s ideas before these unfortunate disciplinary issues came up.
Oh, and no serious academic historian today believes that the Galileo affair somehow indicates that the Catholic Church is inherently incompatible with science. If a historian was to make such an argument, he or she would become the laughing stock of the academic community.
Sorry for the long post!