From an interview in USA Today:
The decision about whether to prosecute individuals wasn't up to him, [Bernanke] says. "The Fed is not a law-enforcement agency," he says. "The Department of Justice and others are responsible for that, and a lot of their efforts have been to indict or threaten to indict financial firms. Now a financial firm is of course a legal fiction; it's not a person. You can't put a financial firm in jail."
From another report:
Asked if someone should have gone to jail, he replied, "Yeah, I think so."
There's a video of the interview at the first link.