If your "take away" is that his message was about free speech alone, you either weren't listening very closely or choose to ignore the totality of the ideas. Stewart's appeal was essentially that tropes, oversimplifications, stereotypes, and prejudices that are "free speech" can and should be challenged by reasonable dialogue based on facts. He implied that sunlight was the best disinfectant, not reflexive condemnation.

Unsaid by Stewart was the fact that reasonable dialog can take place only between people of good faith and mutual respect for the facts. THAT, however, is the problem that exists today. It exists on this message board every day, and it exists in THIS exchange.