In reply to Grimsaburger, who said: "Maybe they just don't get it when no one's telling them when to laugh."
That's exactly what I'm starting to think as well. I noticed, reading one critic, that after bashing Stewart for being too tepid and too nice to Hollywood (clue #1), they noted his few shining moments, which eerily coincided with the moments where the audience laughed the most (clue #2).
First of all, I thought Stewart eviscerated Hollywood; my only worry was that he was being so hard on them that the audience would turn on him. And about the "high points", sure, those moments were funny, but I thought it was fairly obvious that most of the humor (and the sharpest barbs) came at Hollywood's expense, so it would stand to reason that TV viewers would find it funnier than the live audience, which is exactly what one should expect of Stewart.
Of course, if you've become so conditioned by TV that you only know something's funny when the audience is shown a blinking "Laugh" sign, I guess you might not notice.