The Real Story Here
It is not the guns, it is the total lack of real security for passengers getting on the train, and the lack of control of checked baggage that is the real story. Firearms were banned in stages, first after 9/11, and later after the attacks on the trains in Madrid (like making it against Amtrak regulations is going to stop some Mumbai whack job from taking a gun to the train station).
The NY Times, in an editorial today on this Senate action, spills the beans. It appears that random checks of people and baggage are made, but unless you waved your pistole around - or you were caught printing, there is no structured security to keep you off carrying concealed, let alone in your carry-on (or even your checked, for that matter) luggage.
The Times, in its normal anti-gun rant, is against this because it would require the baggage car to be secured, and an airline sterile area appraoch would have to be created for passengers and carry-on luggage.
Banners always seem to be stupider than we think they can be. Bin Ladin and his Merry Band now know how to hit Amtrak (and the commuter rail lines around NYC) courtesy of the NY Times.