As you may have observed, Tom Bradys are pretty rare. So the chances of Flynn turning into Brady are extremely low and I wouldn't bank on that with a big contract. If Belichick had KNOWN what Brady would become, he would have drafted him four or five rounds earlier.
So yeah, as of now, Matt Flynn doesn't have much obvious upside. He wasn't even that good in college (one starting year, bad completion percentage, a manager of a championship team) and that's why he was a late-round pick. We haven't seen enough to say he's any more than he was in 2008--an NFL backup.