That makes me laugh for some twisted reason. :)
Everyone seems to be having a hard time figuring out a good way to deal with the terrorist threat without infringing on anyones rights. That sure does pigeon hole your options and every opportunity available is another door for a terrorist to walk through.
There has to be an answer, somehow.
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.