NYT columnists are not known for lying, but here is an example:
It leaves open the possibility of subjecting American citizens to military detention and trial by a military court.
http://www.nytimes.com/2011/12/16/opinion/politics-over-principle.html?
From the actual text of the legislation:
(1) UNITED STATES CITIZENS.The require-
13 ment to detain a person in military custody under
14 this section does not extend to citizens of the United
15 States.
http://www.lawfareblog.com/wp-content/uploads/2011/12/NDAA-Conference-Report-Detainee-Section.pdf
If one may not be detained by the military, he consequently may not be tried in a military court as well. And the venue is really not at issue, given the fact the legislation in no way mitigates habeas or other due process rights.
The only thing wrong the Administration has done is to poorly handle the politics of the issue.
In 1031 their is no protection from being detained by the military for U.S.Citizens