Passenger rail financial losses are a long and detailed subject - one that I have been involved with for some time - but also, one far too complex to discuss on cycle touring blogs. Suffice it to say that if I had an easy answer, I'd be Secretary of Transportation.
Almost all passenger rail all over the world has some degree of subsidy - but other forms of transportation do, too. Airports constructed at public expense - gate fees are only a fraction of cost. Cruise ship terminals. Etc. Etc. Despite the Highway Trust Fund - automotive transportation gets lots of hidden subsidies, too. That's why so many of us get rankled when people tell us to get our bikes off the road because THEY paid for them.
The only Amtrak route that makes money is the Northeast Corridor. Other corridors - like Los Angeles to Santa Barbara, Eugene to Vancouver - come close. But loge-distance, overnight trains that have only one train each way per day have very high overhead, lengthy schedules, frequent delays, and high overhead costs. Washington to Chicago takes almost 18 hours on Amtrak - a little over an hour by air. Amtrak's travel time is the same as Greyhound's. Round-trip cost - - train - $188, bus - $180, plane - $240.
So even if Amtrak raised its fares to $240, they would still be losing $50+ per passenger and probably more since they would shed fare-conscious passengers to Greyhound. There are no easy answers - and getting bicycle baggage service to Cumberland is not going to be one of their top priorities - especially if it costs money.