He looked pretty good during the 4th quarter of last week's game. Remember, Carson Palmer wasn't the same guy the season after he came back from the same injury... although in Palmer's defense he got hurt in the post-season and Brady got hurt in the first game of the regular season.
I think some of it is that he's not fully back yet, and some of it tonight has to do with the fact that the Jets defense is really, really good. Look what they did to Houston last week, and what Houston did to a pretty good Tennessee defense this week. Brady also didn't have Welker to throw to today, and Welker is like his honky security blanket.