Not really. What you need to realize is that there's three main groups of atheists. One group merely finds that, for whatever reason, they cannot believe in a deity. This sort is usually fairly civil, and rarely uses the "free thinker" label in the way you were describing. The second main group is those that have turned science into a religion, deeming it to have "disproved" the possibility of a deity and thus making all regions invalid (note: atheistic religious philosophies generally fall into the first group, but sometimes fit here as well.) This group often uses the "free thinker" label to denote themselves superior, because "of course" nobody with half a brain cell would call them wrong. By far, however, the derogatory use of the "free thinker" (in the sense that they use it to make themselves seem superior) comes from the third group. This group, best characterised by Family Guy's Brian (and Seth McFarlane himself, for that matter), uses atheism the way a lot of people use conspiracy theories. They try very hard to present that the mere fact that they have discarded religion automatically makes the worst of them morally, intellectually, and philosophically better in every way than the best religious person ever. (I've even seen those that insist Hitler was a better man than John Paul II becuause "at least Hitler didn't rely on a magic man in the sky to tell him what to do."