Therein lies one of the biggest problems of Amtrak. It is charged with becoming self-sufficient and at the same time with providing rail transport to all Americans. They are conflicting goals.It depends on Amtrak's mission. In my opinion, because Amtrak is publicly financed, their rates should be kept at an accessible level for median Americans. If, however, Amtrak's goal is to be self-sufficient, then sure, they should raise rates as high as the market will support. That said, I personally think that because of Amtrak's current structure (being responsible for more than just operation of routes), self-sufficiency is not the right goal to have.
Mind you this isn't something that's unique to Amtrak. This is very typical of the Fed. For example the FAA is charged with both promoting air travel as well as regulating it and ensuring its safety. Again, conflicting goals that often cause the FAA to move to slowly on certain things.