Dinesh D'Souza, author of the recent book What's so Great about Christianity? and who recently engaged in a debate with Christopher Hitchens (I have some disagreements with D'Souza on a few points, but generally he did well) recently posted an article called "Debunking the Galileo Myth" which explains why the usual story passed around about the church's persecution of Galileo is not accurate. Of course, the church did persecute certain people unfairly, but using Galileo as a quintessential example of such persecution is misleading at best.

It's probably a good read if you're not already familiar with the issue. Another good resource on this topic is the first chapter of Philip J Sampson's book Six Modern Myths about Christianity and Western Civilization.