Most discussion currently surrounding the Jets and their failure this season revolves around locker room chemistry, Santonio Holmes' problems in particular. There also were undoubtedly more tangible problems, namely a passing game that could not get anything going, even against bottom feeder defenses like the Patriots and the Giants.
It is difficult to say the exact proportions of tangible problems vs. intangible problems. My inclination, though, is the on field issues fed into the locker room stuff. There have been two times during the season there were stories of turmoil in the locker room. They just so happened to come during three game losing streaks, including the one to end the year. That all died down after the Jets seemed to right the ship.
Despite all of these issues, if the Jets simply avoided catastrophic turnovers that led to points, they would very likely have won games against Denver and Miami and gotten to 10 wins. They quite possibly could have beaten Baltimore to get to 11 wins. A passing game built to take advantage of suspect secondaries against the Giants and Patriots could have made those three games different.
Things certainly need to change on various levels. The most important thing that could take the Jets to a different level is building a more productive passing game. I think Holmes will be back for many reasons, but perhaps the most significant is for all of the locker room issues he caused, he can be a real asset going forward in improving the air attack.