Of course, you do understand that the detainee bill allows any agent designated by the President or Secretary of Defense to declare a person to be an "unlawful enemy combatant." There is no reason this can't be done to a US citizen. After that, you get a military tribunal which can allow secret evidence (which you can't examine or refute) as well as confessions given under duress (including torture).
Then you obviously haven't read the bill. This has been beathen to death elsewhere, but the bill specifically does not apply to US citizens. Its written as plain as day. This kind of makes all of your fears irrelevant.
Furthermore, the DoD wasn't exactly forthcoming about who they are holding at Gitmo. They only released a complete list of names under court order. And if you believe there aren't people being secretly held elsewhere, I have a bridge to sell you.
So what if they are. You don't think that the department of defense has reasons for keeping what they do under wraps. And again, people went through the courts and recieved redress. Thats how the system works.
Furthermore, I am aware of at least 3 US citizens who were detained for some substantial time without recourse or access to a lawyer. Hamdi and Padilla are still in custody, I believe (and may well be guilty). Another (a lawyer in Oregon) was in no way connected to terrorists and was eventually released.
And these 3 have subsequently prevailed in court. Whats the point. Out of hundreds of prisoners, you are going to have people who shouldn't be there. Its simply the nature of numbers. When we find out who these people are, their grievances should be addressed. However that doesn't mean that we scrap our whole system.