Besides the blanket answer of "He's just not very good at basketball," there are a few other things that hurt him.
-He doesn't handle physicality well. Despite his size, he doesn't play very strong. He gets pushed around fairly easily. His best games in college were mostly against mediocre to bad teams. When UConn played against a team that had anything resembling legit big men, he usually struggled.
-no instincts. You can get away with not playing strong if you have great instincts. He does not have any.
-Poor BBall IQ. From everything that you read he is a fairly intelligent guy and I don't think work ethic has ever been an issue for him, but so far he just hasn't been able to translate what he learns in practice onto the court in actual games. I hate to jump sports, but former Vikings QB Tavaris Jackson was like this. He was a student of the game, could point out things while watching film that would really impress you, he'd look real sharp during practice, but it all fell apart on the field during games.
-No offensive game. This was known when he was drafted, and it hasn't really changed. I think in a best case scenario Thabeet was only going to average 8-12ppg in his best years.