In all reality, I don't think you'll ever see TSA or similar screening at bus stations, train depots and subways. Congress and the American people wouldn't stand for the expense involved. Chertoff has already said that these transportation venues are pretty much on their own, and he won't commit DHS (read TSA) to providing security.

I think the reason for the focus on aviation as opposed to any other means of transportation is because the idea of flying bombs has a much more devastating impact than a blown up bus, train or subway. Hate to reduce this down to a matter of acceptable and unacceptable casualties, but that's essentially what it all boils down to.