Jon Stewart actually covered this in his podcast.

Basically, Apple gave him editorial freedom and the ability to put his message out there. You have to pick your battles, and he shit on apple a bit during his show and podcast.

He did what he could. When Apple asked him to compromise on his rhetoric, Jon said "fuck you" to which Apple then cancelled the show.

This is a paraphrase obviously.

Jon is a fucking hero for putting his morals first. He is also pragmatic. But he didn't cowtoe to Apple when push came to shove.