The Patriots are not done! And this is coming from a die-hard Colts fan. Sure, Tom Brady going down may knock the Pats out of the 'elite' group in the AFC, but, at least in my opinion, they should still win their division. They no longer have the best QB in their division (obviously Brett Favre, but I wouldn't be surprised to see Matt Cassel surpass either Trent Edwards or Chad Pennington), but they are still arguably the best in their division at every other position (RB may go to the Dolphins if Ronnie Brown is healthy, OL could end up with the Jets if all the new pieces mesh well, and LB is debatable between many teams but i still give the edge to the Pats here). Peyton Manning is not the Colts, Tom Brady is not the Patriots. Obviously, being the 2 greatest QB's in the game today, they are HUGE parts of their team, and would/will be sorely missed. But the QB position isn't the only thing that makes either team great.
So don't try and tell me that a team with Randy Moss, Wes Welker, Laurence Maroney, a great OL, and a top 10 defense isn't going to compete for the playoffs, even with a backup QB at the helm. Especially when there is a brilliant (albeit total d-bag) coach running the show. The Pats are still very much alive.