The Justice Department has filed a brief that address, in part, the question of whether the new TSA procedures are permissible under the Fourth Amendment.
A copy of the brief filed in the Court of Appeals is on Wired. Warning: you have to wade through a lot of administrative law to get to the Fourth Amendment stuff.
The government claims that it is entitled to "significant deference" in its security decisions. This is true, but difficult to assess without a security clearance.
The interesting factual claim is that "the severity of AIT screening procedures' interference with individual liberty is limited." This may be too much, as the public response demonstrates. A better claim is later in the brief: "AIT screening [is] as minimally intrusive as possible to effectively detect the threat."
For a doctrinal standpoint, I think it is interesting that the government barely mentions the idea that passengers consent to a search by attempting to board a plane.
For what it is worth, as I have mentioned before, I think the TSA has not violated the Fourth Amendment. (That does not mean I think they have a good or effective policy – I leave that for others.)