He's in entertainment, he comments endlessly about policy. You think he somehow missed the #1 policy initiative of his employer?
He is very well paid, with a large budget that employs a lot of people. But I don't think his show breaks even on its revenues, it is a tent-pole for his channel. He's paid not for his own audience but the larger strategic benefit he brings to his employer. So think on what might happen if he starts to pose still larger strategic problems for that employer? And what happens to Mr. Stewart should he want to move on from his current perch? [EDIT: As suggested below, the 'strategic benefit' payment is speculation. Probably a mistake to go there, b/c I think my point still stands: if he hurts a major legislative initiative of his industry, his life gets a lot harder and riskier.]
And while he himself seems reasonably secure, he has a staff of writers and producers, many of whom would like to move on to bigger and better things. Who will be greenlighting those various ventures?
Remember, Hollywood blacklisted people for (alleged) Communism. Those people lost their whole careers. Imagine what might happen to those who challenge the studios' interests still more directly.
I'd say this is the perfect moment for Mr. Stewart's reputed bravery, independence and courage.