I do agree with the ACLU in that the searches as currently performed do absolutely nothing to shield us from terrorism. But from a Constitutional standpoint, I do not see how the random searches are any different than "roving road blocks," where cops randomly pull over drivers without any probable cause in the hopes nailing a drunk driver. Much to my disgust, the SCOTUS has repeatedly upheld roving road blocks and I don't see how the random mass transit searches are any different.
That's a very good point. I don't think a roadside checkpoint of any kind can pass legal muster unless they stop EVERY driver, and not just random ones (this was the basis of a decision in a landmark case in New York or New Jersey a few years ago, in which a random drug-enforcement checkpoint on the George Washington Bridge was determined to be illegal).