I found the text of the bill, and below is the language in question (Section 1031 of Senate Bill 1867, the National Defense Authorization Act for 2012). My reading of this: it authorizes the President to use military force to go after the 9/11 terrorists, al-Qaeda, the Taliban, or others associated with them. Assuming that the last part of that is faithfully followed, I don't have any problem with this. If a member of the Taliban happens to be an American citizen, I still want the Marines to put a bullet in his heart. I believe our military is far better equipped to deal with many terrorist attack scenarios than our police forces are.
If I'm interpreting the hyperbolic fire-breathing of those wailing about this correctly, they're afraid that just about anybody could be accused of collaboration with al-Qaeda or the Taliban, and would then become subject to indefinite military detention (or even direct military action). I understand this fear, but I don't think this bill significantly expands the probability of such a thing. Both Bush and Obama have unilaterally asserted all sorts of Presidential powers that reasonable men believe were not theirs to grab. For example, it's not at all clear that Obama actually had the authority to order U.S. troops to fight in Libya. There has been precious little resistance to any of these power grabs. Even in the absence of this bill, if Obama decided to incarcerate (let's say) some citizens of Detroit accused of being al-Qaeda funding sources in Guantanamo, do you really thing the absence of clear authority would stop him? I do not, nor do I think it would have stopped Bush.
So I think this is much overblown...
SEC. 1031. AFFIRMATION OF AUTHORITY OF THE ARMED FORCES OF THE UNITED STATES TO DETAIN COVERED PERSONS PURSUANT TO THE AUTHORIZATION FOR USE OF MILITARY FORCE.
(a) In General- Congress affirms that the authority of the President to use all necessary and appropriate force pursuant to the Authorization for Use of Military Force (Public Law 107-40) includes the authority for the Armed Forces of the United States to detain covered persons (as defined in subsection (b)) pending disposition under the law of war.
(b) Covered Persons- A covered person under this section is any person as follows:
(1) A person who planned, authorized, committed, or aided the terrorist attacks that occurred on September 11, 2001, or harbored those responsible for those attacks.
(2) A person who was a part of or substantially supported al-Qaeda, the Taliban, or associated forces that are engaged in hostilities against the United States or its coalition partners, including any person who has committed a belligerent act or has directly supported such hostilities in aid of such enemy forces.
(c) Disposition Under Law of War- The disposition of a person under the law of war as described in subsection (a) may include the following:
(1) Detention under the law of war without trial until the end of the hostilities authorized by the Authorization for Use of Military Force.
(2) Trial under chapter 47A of title 10, United States Code (as amended by the Military Commissions Act of 2009 (title XVIII of Public Law 111-84)).
(3) Transfer for trial by an alternative court or competent tribunal having lawful jurisdiction.
(4) Transfer to the custody or control of the person's country of origin, any other foreign country, or any other foreign entity.
(d) Construction- 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.
(e) Requirement for Briefings of Congress- The Secretary of Defense shall regularly brief Congress regarding the application of the authority described in this section, including the organizations, entities, and individuals considered to be `covered persons' for purposes of subsection (b)(2).