There is a post on the Northeast portion of BikeForums about bikes and Amtrak. They are not very cyclist friendly. I think they allow bikes in the baggage area of some stations (from what I understand of some of the posts). A few wrote letters to Amtrak complaining.

If you find out anything, let me know. I am very curious. One day we would like to travel by Amtrak with our bikes to Washington DC.

JoAnn