as I've already posted in this thread, amtrack and gray hound have a no fire arms policy, this includes checked bags.
Most mastransit have no gun policy as well.
So what could happen to you is going to depend on the state/federal laws. If make it on to a train with a gun, I could very easliy see you being charged with tresspassing in federal court, which is a felony btw.( its a very old law)
Remember though that in many states, (CO, WY, UT) That new castle doctrine laws override many of these old policies. States that have pulled their heads out are recognizing peoples RIGHT to self defense. Some are even starting to understand that the reason that this right was granted us in the constitution is so that the government CAN'T tell us where and when it's ok.
I understand what you are saying, BUT this will probably be one of the next battles. Based on recent SCOTUS rulings.
Basically, if the constitution allows me the right to defend myself, (and the supreme court has said this) then the government has no authority to restrict WHERE that right is applicable.