Headless, your analysis of the problem is fundamentally misguided. Your stuck on what you think the perceived facts of each detention will be - if only bad people are detained, you're fine with it, and that's different from a policy of detaining political opponents.
Here's what you missed, and the key problem with your support for unlimited detention: In the criminal system, the government has to allege facts and prove them beyond a reasonable doubt. This is how you ensure that the bogey-men like Padilla go to prison, while the political opponents like gun owners do not.
Now, under Bush, you supported giving the government the power to use a label (terrorist) to detain anyone it wants, and to deprive that person of any right to challenge the detention. Knowing that Bush would not always be in office, what mechanism do you then have for only ensuring that the Padillas go to prison, and not the run-of-the-mill gun owners?
Answer: None, because there's no review process and no check on the government's power. It just says "terrorist", and that's the end of the story. This is the problem with relying on the rule of "when headless thinks it's okay to arrest and detain it is, and when headless doesn't, it's not" to guide your approach to to this issue. It's an institution that exercises the power, not a person, so unless you have a reliable mechanism to monitor and restrict its activities it absolutely will imprison people that you feel insulted at having to compare with Jose Padilla.
Sometimes you need to focus less on what you think are the facts of each case (because in reality, you don't have any clue what Padilla did personally), and more on how the process for determining right from wrong works in order to get a decent result. Tossing out important restrictions on state power because you hate the accused today is a guaranteed mechanism of facing gross injustice against someone you don't hate tomorrow - and this bill is proof of that.