Phil Carter does a pretty thorough job of discussing the Padilla case, but I have to agree with JAG Central that the key to the case is whether or not Jose Padilla is an enemy combatant or not.
Since the FBI found Padilla's application to the al Qaeda training camp in a binder that contained 100 other such applications, type-written each with the title at the top, "Mujahideen Identification Form/New Applicant Form," I don't see how you can argue he wasn't an enemy combatant. And if he's an enemy combatant, then the whole panoply of American rights goes out the window. Period. End.
It's important to remember that it was al-Qaida, and not George Bush or the US military that turned our country, along with every other country, into a battlefield. Jose Padilla was an enemy soldier trying to infiltrate our lines to kill civilian non-combatants. Now we can decide that it is better that 99 enemy soldiers go free than a single innocent be wrong classified, but let's be honest about it. We're betting lives on our ability to be near omniscient and omnipotent, and I don't think our track record is that good. If you found an enemy soldier infiltrating your lines, would you prefer to act immediately, or wait until you had enough evidence that you could take to court?
If we adopted the standard that once an al-Qaida operative was in the US, and a US citizen, we had to work through the legal system, what kind of pressure would that place on our defenders? Waiting for a crime of mass murder to be committed while they just watched and waited and hoped they could stop it in time. Wouldn't it be easier (and better) to just make those people disappear with no accountability? Questioned and then killed? Just how badly do we want to tempt ourselves?