Typically, the NCAA will grant waivers to players who have already graduated to allow them to transfer and play right away if their field of graduate studies is not offered at the player's first school. That is the case with Masoli, but the NCAA can see that there's more to his case. He got in serious trouble with the Oregon program, and while he wasn't outright dismissed, you don't have to be a rocket surgeon to figure out that he didn't transfer the Ole Miss solely for academic reasons.
While Masoli met the letter of the transfer waiver rule, he obviously didn't follow the spirit of it. Ole Miss is appealing, of course, and if the appeal is denied as well, Masoli will red shirt and be able to play in 2011.