I've spent the better part of the last week looking into this issue. It's a complicated subject that's being massacred by media sensationalism. They paint with broad strokes of black and white, and invoke the specter of totalitarianism. And that's when they don't outright print falsehoods; the latter article makes scare talk out of an amendment that never made it into the bill, for example.
They're not wrong to be disturbed, though. Here's what I've found in my checking:
The disputed section is Section 1031 of the National Defense Authorization Act for Fiscal Year 2012 (henceforth NDAA). Section 1031 allows the military to detain:
-Anyone involved in any way with the people who orchestrated 9/11;
-Any member of Al Qaeda, the Taliban, or 'associated forces';
-Anyone who has offered 'substantial support' to the above;
-Anyone who has 'committed a belligerent act or has directly supported such hostilities in aid of' the above.
Detainment is pending disposition under law of war, which can be:
-Held until the end of "hostilities" (as defined in the Authorization for the Use of Military Force in 2001);
-Trial under Uniform Code of Martial Justice or other competent court/tribunal;
-Transfer to custody of a foreign country or entity
People will tell you that this section exempts US citizens and lawful resident aliens. They are wrong. The section with that exemption is 1032, which requires the military to detain certain people who have been captured in the course of hostilities. Nothing in 1032 removes the military's authority to detain citizens or resident aliens.
The first important aspect to consider is that the authority for this provision comes from the Authorization for Use of Military Force signed in 2001 (AUMF). You'll notice that the AUMF doesn't exempt US citizens either. In truth, the NDAA isn't granting the executive any special new authority; it is actually clarifying the extent of the wartime powers granted to the executive and the military by the AUMF. This was particularly made explicit by a last-minute compromise amendment from Senator Feinstein, which inserted a clause saying "Nothing in this section is intended to limit or expand the authority of the President or the scope of the Authorization for Use of Military Force."
The executive gaining more power in wartime--even beyond the bounds of the Constitution--is nothing new. Practically every conflict in the last century has involved something of the sort--the most famous example that comes to mind is Executive Order 9066 and the Japanese-American internment during WWII. One difference between that time and this one is that WWII was the last time the US was legally in a state of war; the Authorization for Use of Military Force is a watered-down state of affairs that we've used for pretty much every military action since then.
The more troubling difference is the amorphous nature of the enemy identified in the AUMF. Not only nations, but organizations and even people are targeted. And the victory condition--making it so that none of these nations/organizations/people can orchestrate any more terrorist attacks on the US--is incredibly vague. It's not like Al Qaeda is going to strike their colors and let us know we've won.
In the immediate term, the concern is that anyone, even a US citizen, can be detained on suspicion of supporting terrorists and held indefinitely, even turned over to another country and squeezed--ahem, tortured--for information. Legally speaking, most people who are detained in this manner can apply for habeas corpus review of their detainment...but tell that to Maher Arar, a Canadian/Syrian citizen who was detained at JFK Airport in NYC; rendered to Syria for the better part of a year, during which time he was tortured; and remains on US watchlists to this day, despite being publicly exonerated of any connections to terrorists by both Canada and Syria.
In the long term, there is the broader concern of how much wartime power we can afford the executive branch, and for how long. With no clearly defined achievable end goal, there is the real possibility of indefinitely maintaining this state of pseudo-war, and thus the extraconstitutional authority of the executive. Obama's response has been instructive: in the White House statement threatening to veto the NDAA, he called the provisions "unnecessary, untested, and legally controversial restriction of the President’s authority to defend the Nation from terrorist threats." (emphasis mine) And the White House was responsible for removing language from Section 1031 that would exempt American citizens and lawful residents from the authorization to detain. See the Senate session video record, at 4:43:29; Senator Levin explains.
On the other hand, Obama's statement also refers to "...the fundamental American principle that our military does not patrol our streets," and how the current bill "would tie the hands of our intelligence and law enforcement professionals." He is simultaneously objecting to the restriction of executive authority, the required use of military custody under 1032 rather than other forms of custody, and the disruption of existing executive/judicial doctrine on who the AUMF applies to. So from a rights perspective, it would depend on what the existing doctrine is; unfortunately, I haven't been able to find out. In the executive authority column, Obama is solidly 'for'...but that may only be because Congress is usurping his role as Commander-in-Chief by mandating who the military must detain. After all, that's just another way of saying "who must be detained by the military"...as opposed to detainment by law enforcement or intelligence.
Basically, there are a whole host of reasons why this bill is bad legislation, even beyond the human rights perspective. But it got through the Senate 93-7, and now the House gets to take a look.
Let's be clear, I'm not worried that the military is going to go out and start locking up random American citizens on fabricated charges of terrorist conspiracies. I'm worried that the military is going to approach these detentions with sober well-intentioned consideration...and still get them wrong. And I'm worried that 'wartime executive authority' will eventually become just 'executive authority', an extraordinary measure maintained long past all justifiable cause, until it becomes the ordinary state of affairs.