Amtrak is subsidized heavily by the gov't/tax dollars. if it lowers prices guess who pays. kind of like metro. metro loses $ on every trip.
One of the main problems here is the stupid government doesn't know how to run a railroad. Lots of Amtrak routes are profitable...but in order to placate congress they have to keep open a bunch of routes that lose all the money. It's stupid politics.
The Acela alone is profitable enough to make up for the losses taken on many of the routes, but not all of them.
Edit: By my quick calculation eliminating the 14 lowest performing routes and amtrack would break even. Of course you need to balance this with ridership...some of those 14 are very under-used, some not as much. The point is there is a road to sustainability for Amtrak if they balanced the business aspect AND the service aspect.