While Jon has proven to be quite the interviewer and critic of the popular media. This job would effectively end his role as a satirical commentator that has made him so popular. There is no expectation of him at Comedy Central to work with real news. Granted his show does lampoon quite regularly the laughable state of affairs we find ourselves, but in jumping ship to NBC he would quickly find himself having to anchor a ship with much larger problems than just the one show, Meet the Press. The comparison of Colbert going to CBS's Late Show is not the same, sure Colbert gets to still be a funny man, but he is going to a winning franchise, not having to reinvent it as they'd expect of Stewart.
It's not like he really needs the job. I think he is doing just fine with what he is doing now. I think him joining meet the press would have been good for them, but I doubt it would have been an actual gain on his end. Not a bad or good move.
As his now more than decade-long career as a successfully television personality proves, Jon Stewart is not a dumb man. He knows how media markets work, and he knows that he's got a good thing going at Comedy Central. He has a large and dedicated young audience, he has a TV time slot that best suits that demographic, he has an established TV show format that works very well for his strength and the needs of an audience, not to mention a very supportive network that allows him to do just about anything he wants. Indeed, you would be hard pressed to find a more permissive TV network, given that the ratings are there. Stewart knew that at ABC, almost none of these things would be true.
Jon Stewart has a huge following from the younger generation. Meet The Press is an older generation news program. If Jon Stewart would have accepted the position, he would lose a huge percentage of his credibility with the generation he has as fans. It may seem to some like a bad move, but in the long run, Jon Stewart will have many other opportunities that will allow him to keep the fan base that has built him high in public opinion.