Bill of Rights issues are often tested on the worst possible defendants, and Padilla's case is an excellent example. On the one hand, this would-be Al Qaeda terrorist is the kind of person nobody wants to defend. On the other, he has the same rights as everyone else else, and there appears to be no evidence of a serious crime.
Padilla seems to be a dangerous person (or at least he was before all this), so giving him a chance at freedom doesn't seem like a good idea. But it would surely be much more dangerous to allow the President the power to arrest and imprison American citizens without trial, merely by designating them enemy combatants. That would be precisely the kind of arbitrary use of power the Bill of Rights was created to prevent.
I am reminded of the Night of the Long Knives in 1934, when Hitler killed about a hundred people, mostly Brownshirts, his own unruly followers. This met with no protest, because the lawless Brownshirts were generally feared and despised by the public . . . But the silence of the "respectable" Germans was a mistake, because if Hitler could ignore the rule of law in this case, he could do it in all cases: If the law did not protect Brownshirts, it protected no one.