My problem is Stewart is the same one I always had with Al Franken, which is that they have their moments where they make an attempt at serious journalism and reporting, and at times express a desire to be taken seriously in such endeavors, but at the same time, they are allowed to exaggerate and mix up facts and truths, and say it's ok because they are comedians, and you are at fault for trying to take them seriously in the first place. This was brought up at one point in the interview, but I think Stewart largely dodged the issue. At least Stephen Colbert realizes that his show is an unabashed farce and a parody and at no point attempts to be taken seriously.
For a very large percentage of the American public, the only exposure to what is going on in the world of politics (sadly) comes from Jon Stewart, and I think he has a duty and responsibility to stop blurring the lines between journalism and comedy. While it's certainly not his fault that so many people are ignorant enough to believe that he is actually reporting the news, it is still his burden to bear.