I think it's time to recognize the following things.
1) It isn't clear "how bad" Padilla was or would've been.
2) The administration has no real evidence about how bad his ongoing associations were.
3) They had no evidence that he had any specific plans. The confessions he's made since may or may not have any basis in reality.
4) Even if Padilla was "bad," putting him on 24/7 surveillance and using that to track down his connections would have been much more productive from an intelligence standpoint than holding him for 2 years.
5) If they can do it to Padilla, they can do it to you.
And don't forget, it's John Kerry Thursday.
Melanie at Just a Bump in the Beltway looks at the Padilla thing too.