I'm not a QB coach, but I've watched Brady since he was at Michigan. I think he's progressing, but I don't think it's the same problem from week 1 to now.
The first few games, he didn't seem comfortable in the pocket at all. For most of the Bills and Jets games, he seemed jittery by his usual standards. For those first two games, he was extremely inconsistent. Short, intermediate, long, it didn't matter. He would throw one way while the receiver went the other. But he seemed to settle down in the Atlanta game.
Once he settled down, he had better success with the short and intermediate routes, where he can rely on his arm only. This is when the team started moving the ball well, and we started to see more TDs in the red zone as Brady could complete these short passes consistently.
However, the one area that he's really struggled all season is the long ball. He's consistently overthrowing receivers, and the ball often sails high because he's throwing off his back foot. If you watch the Broncos game, Brady never comes close to stepping into that ball to Moss that would have been a TD.
Pure speculation here, but it seems like he doesn't want to step into it because his front leg will be locked for a few seconds, which is how he got hurt last season. I don't know what happens in practice, but I wouldn't be surprised if he's making these throws just fine.
I've heard speculation about his arm and shoulder from the Haynesworth hit, but those seem fine to me. His throws have good velocity and the ball remains in a tight spiral, even on deep balls. The majority of the misses are overthrows. I can only think of one throw that didn't have the velocity to get there, the long ball to Galloway vs. the Jets that would have been a TD, but it floated and a Jets DB caught up to knock it down in the end zone.
The good news is that the speed of the game doesn't seem to be overwhelming him, his decision-making looks great as he's often going to the right receiver (though against Denver, he seemed to look to Welker's way only at times), and his arm strength seems pretty good to me. So all of the problems are not permanent; they can be corrected.
I'm really not that concerned about Tom. Yes, it's frustrating. But I remember him as the 7th-string QB at Michigan at one point. The guy knows how to overcome adversity. He'll be fine.