Stewart has repeatedly taken the view that it doesn't matter what people say/write/draw/etc., so long as they might argue that it was just a joke, just art, just pop culture, or whatever.  So of course he criticizes people for getting all worked up about the New Yorker's Obama cartoon.  "It's just a cartoon."  "Only extremist Muslims get all worked up about cartoons."  Inexplicable.
Hard to imagine Stewart -- who is clearly a smart guy -- could be so stupid on so basic a point.  Forgive me for stating this explicitly.  One doesn't expect that adults need to be told this:  Yes, it matters what people say, whether they're joking or not, because what they say may affect people's opinions, and people's opinions affect what people do, and what people do can either make life better or make it worse.  The effect gets scaled up or down depending on how widely distributed the speech/writing/painting/tv show/whatever is.
My apologies for leaping to the obvious, extreme example, but the Nazi cartoons of the brutish-looking, big-nosed Jewish vulture or jackal assaulting a virginal Arian were intended, in part, to be funny -- the big noses, the fangs, etc.  And yet they mattered.

Because the real alternatives are so good (because McCain is so close a second-place to Obama);

Because the stakes are so small (because globally catastrophic climate change, smart and effective national security, officially codified torture, a counterproductive, stupid, and feckless war, and plutocracy are not at issue this year);

Let us nurture our political purity and join the right wing in criticizing Obama.  Let us refuse to fund his campaign.  Let us vote for Ralph Nader.

What's the worst that could happen?