Think about it: Most folks have no problem getting searched at a stadium, nightclub, or similar venue, mainly because they consider this part of a "voluntary" transaction of sorts -- and the government isn't really involved at all. On the other hand, a lot of us despise the idea that something as incompetent as a government would be involved in "violating" our rights simply because we have an expectation of being "free" to use something like a subway or bus with minimal interference.
The obvious solution to this dilemma is to get government out of mass transit entirely, and stop treating it as if it were a public commodity. Let a private operator take over the subway system, and let that operator figure out a way to deal with security matters.
Of course, this also requires us to treat the subway system as a fully private system and get rid of this silly notion that being "open to the public" automatically means a private business must function as if it were operating in a public space. If the subway operator wants to prohibit all packages, bags, etc., then so be it. They should also be permitted to refuse entry to anyone who "looks suspicious" or for any reason whatsoever, which means they cannot be sued just because they turned away some swarthy guy in his pajamas wearing a long beard on his face and a diaper on his head.
The airlines are private entities. How's that working for them?
You make a great deal of sense here...unfortunately there are far too many nanny-staters (especially here on FR) that believe the silly notion of "being open to the public" means it is public space.