"Now the question: Is there an atmosphere of intolerance that keeps a certain portion of users from feeling free to express themselves?"

Yes, there can be. If you disagree with the wrong person, or you express an opinion or view that is considered unpopular or not held by the majority there can be a backlash that can get you labeled as a troll, get you shunned or intimidated, or made a target of constant sarcasem, ridicule or animus. It's unfortunate, but that's the way it is. There are those that would prefer to remain in the shadows than be the target of the mob armed with pitchforks and torches and screaming for blood. ;)