I hate to have to make comparisons like this, but it feels sometimes like we're slipping more and more toward the 'anti-freedom' that we had such a problem with in the former Soviet Union and eastern European countries (and to some extent, China today). Just a few years ago, most people would have thought it crazy to even hear serious talk about 'national ID checkpoints,' but it was one of the 9/11 Commission recommendations, and there has been at least one senator (that I know of) who's come out in favor of such.
As to what JLo (first) said, I would say that the Constitutional basis for denying a search would be the implicit right to privacy we have, and that the 9th Amendment was supposed to ensure, though the courts have vigourously disagreed with my view of that. I love your point about a popular outcry being the wrong reason to do it, though.
To Mahoot: And what do you when officers start checking you when you're walking along? It's not the reality yet, but it's something that isn't too hard to imagine a few years (or less) from now. (EDIT: And to what you later said, do we have a Constitutional right to breathe? Or to walk around without being stopped and searched? It's not explicit, but the 9th Amendment is supposed to ensure that just because it's not listed, doesn't mean it's not a right. I feel that a "right to use mass transit" falls in the same boat.)
As to a point of difference between airlines and railroads (such as NJT, Amtrak, or the LIRR), the airlines are privately owned, and as much as I hate the "rights" corporations have, they can basically do whatever they want to your luggage and you have little recourse. I dislike that the federal government interjected itself in the matter, but if the airlines had gone to the government, asked for help, and gotten it, you'd be in the same spot as if it were all private. Railroads, at least in this area, are state agencies, or at the very least, depend heavily on government subsidy for operations and improvements. With money coming from the NJ state legislature earmarked for particular NJT improvements (when it does come, anyway), to me that's as good as saying that the railroad is a state agency, which would then make it subject to the same restrictions on searches, etc. that law enforcement would be subject to (especially since NJT/MTA police are recognized law enforcement).
Now that I've got all that out, I'd be happy to take this discussion to e-mail or PM if it's too off-topic/inflammitory for here. If there's enough interest, I can set up a mailing list so everyone can get in on the fun.
Overheard in NY Penn: "All aboard! Get on the train if you're coming with us!"