You can definitely take a folding bike on Amtrak, and it does not have to be bagged.
Read this article:
http://www.bikefriday.com/amtrak
Download and print out the conductor rule page PDF and carry it with you:
http://www.bikefriday.com/images/new...akpolicy07.pdf
Although the conductor still has authority, particularly if the baggage area is full, Amtrak now (as of May 2007) has clarified the policy and specifications in the above PDF. I have done over 75 round trips on Amtrak with my folding bike this year!