I think my perception probably has to do with how Keller has gotten his numbers. There have been some huge games and some very quiet ones. Perhaps things would be different had he accumulated his numbers in steady succession through the entire year. Things average out, though, to put Dustin pretty high and more productive than most tight ends.
I am not sure he is entirely to blame for his relative struggles in some games. The Jets have gotten very hot and cold quarterback play. He also has been the primary target in some games, especially early, and an afterthought in others. When he has been the first look, like early in the Bears game, the Jets have moved the ball well through the air.
If I was running the offense, I would run the passing game through Keller. His athleticism makes him a very difficult assignment for most linebackers. If the defense uses one to cover him, there will be some easy completion. If the defense uses a safety, either Braylon Edwards or Santonio Holmes will have a corner without deep help. If the defense takes a linebacker off the field in favor of a nickel to cover him, it is time to start running the ball with less big guys in the box. There are other effective approaches. This is just the one I would use.
Putting up those numbers in his third year is promising. He still has time to get better too. I have noticed his run blocking and route running have improved greatly since he entered the league. So let me tip my cap to the starting tight end.