I've done quite a bit of multi-mode commuting / travel with Amtrak, Greyhound, Metra and South Shore (the last two in that list are regional commuter trains in the greater Chicago area).

My folder is a Dahon Boardwalk S1 (20 inch wheels), and I use Dahon's El Bolso carrying bag. I've never had trouble getting my bike onto any of these options. The only headache I've had is that at 30 pounds it can be a bummer getting my bike onto an overhead luggage rack... especially when I board a train late at night and folks are sleeping. But, it's easy to get the bike in underneath luggage space on Greyhound, and I can usually find floor-level luggage storage on Amtrak.

I've written more detailed accounts of my experiences on a bike-advocacy blog, if you're interested:

http://bikemichiana.org/tag/monkey-bike-chronicles/