I still don't understand what the problem is. Of course no one likes paying higher fares. But these practices are entirely consistent with the long-term trend of Amtrak chasing yields in an increasingly aggressive manner. They have little choice but to charge whatever the market will bear as demand outstrips supply (i.e. their fleet, which is not growing fast enough relative to ridership) and operating support from Congress remains uncertain. The only problem would be if fare increases caused lower revenue/ridership/revenue-per-seat-mile.

Even if it was an airline, the answer to "Why are they charging higher fares?" is always the same: "Because they can." Isn't that FT 101?

Silver lining: At least higher fares make AGR points more valuable.