I wrote and investigated this as a response to something a friend from Facebook pointed out: there's a provision in the bill in D.1032.b.1 that says explicitly that American citizens are exempt from this bill that would, supposedly, allow the US military to indefinitely hold American citizens without trial. There are a couple of different factors happening here, some of which are irrationality and ignorance.
My personal opinion (not culled from research) is that the US government has shown how much they care about our right (of the press) to free speech with how they've reacted since 9/11 and with press at all the Occupy sites. In short: not very much. Therefore a bill that allows indefinite imprisonment without a trial (even though it specifies it's non-applicability to US citizens) that uses the military as a police force sounds like a bad idea that could be easily fudged to support the agenda of the government.
Having said that, there are some problems with the way in which this bill was initially drafted (in secret by McCain and Levin). This guy (who's as crazy as a site named "Texas GOP Vote" can possibly be) initially reacts to the fact that the bill was written in secret. He doesn't mention it here, but the bill was passed without a single hearing, and the media has blacked out coverage on this story (link). So, the secrecy of what's happening borders on illegal while the media blackout is scary given that the majority of citizens still get their news from major media outlets. At least those people that didn't grow up with a computer in their living room. Either way, it's a frightening proposition that a significant portion of the population that doesn't read news on the internet or from alternative sources could be so terrifyingly ignorant of what's happening. But not because they don't read the news, but because they get it from a major source.
The next thing is that apparently during the debate itself over the bill, senators disagreed as to whether or not it would apply to American citizens. After all, There's a prevision (D.1031.a) that gives the president the right 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." Later on in the bill is a section saying (D.1032.a.4), "The Secretary of Defense may, in consultation with the Secretary of State and the Director of National Intelligence, waive the requirement of paragraph (1) if the Secretary submits to Congress a certification in writing that such a waiver is in the national security interests of the United States." Paragraph 1 is all about the military holding people until "disposition under the law of war." If I read this correctly, this is essentially the basis for secret and indefinite arrest. But the most concerning is the part where the President gets to do whatever's necessary to protect America's interest. It wouldn't be difficult for the president to decide that this particular American is a big enough threat that D.1032.b.1 can be waived.
As I said, even the senators disagree. Once again in this article (link), Graham says that it absolutely applies to citizens and turns the homeland into the battlefield. The Russians have the motherland, the Germans get the fatherland, we get the homeland. The situation with this guy is that he could just be wrong. He could be so ridiculously wrong about the super super obvious - the bill doesn't apply to American citizens - but the fact that he even wants it to apply to citizens shows that there is a wide margin for abuse. The same article describes that anyone who provides aid or information to a terrorist qualifies as a terrorist under the Patriot Act, thus the NDAA potentially opens the door even wider to allow for people's actions to be interpreted as terrorist aid.
But the most worrisome element of all is precedent. There is already precedent for American citizens being denied fair trial in the interest of "national security." There is Anwar al-Akwali who was the guy on YouTube who preached in favor of Al Qaeda. The situation here is a lot of speculation, but General Dunlap said that he views American citizens overseas speaking against America as enemy combatants. Al-Akwali was an American citizen, so theoretically, he should have been put in custody and taken back here for a proper trial. This blog discusses that in the first draft of the bill, it absolutely would/could apply to citizens, but in the new bill, the provision was stuck in. He isn't very convinced that it still won't apply to citizens, and he also quotes General Dunlap saying that the Authorization of Use of Military Force Resolution of 2002 (look this sucker up on Wikipedia. The author at Lawfare Blog doesn't cite this specifically, but I looked and found what the AUMF was, and what he was talking about) classifies Americans overseas as possible combatants.
A lot of what's happening, both in the senate chambers and the news sphere, is uncertain speculation and a little bit of fear mongering. But ultimately, there is strong precedence set forth in which 1. our rights have been ignored (both now and in the past: Japanese internment camps; McCarthy hearings; repeated denial of the press); 2. Americans have been and could be detained or executed without a trial; 3. the government has shown intention of extending the war to its citizens (in both the former form of the bill in which McCain wanted to be able to pursue American citizens directly, and the AUMF).
In thinking about the bill and the fact that 93/100 voting senators passed it, I can only come to the conclusion that there are two types of people voting in favor of it: 1. The exceptionally terrified senator that thinks either the Devil or Osama is hiding under every rock, or 2. The senator that has been bought and sold. There's a lot of money to be made in both war and detention.
Added note 12/15: this thing passed yesterday 283 to 136. That is very sad.