Between usurious property tax at the state level, and the machinations of the former ICC, whatever value that the Railroads got for that land has largely if not completely paid back in public goods. Furthermore those landholdings are largely long gone too.
Consider how long railroads were required to offer service that was unprofitable, underutilized, or forced to price itself in an uncompetitive way - all in the name of the public good.
While I think both BNSF and UP (as well as CSX and NS) have an obligation to make sure Amtrak can run on time an under a reasonable schedule. Also, if the railroads dont like it, the alternative is being forced to resume operating the passenger trains they were operating in 1971, and continue to operate that or a similar network in scale and size for at least 10 years without subsidy.
The interesting thing about Amtrak is, if USPS had continued to route first class mail by train, Amtrak might not exist, it was the removal of the indirect subsidy - which turned passenger trains from a break even proposition, which helped generate goodwill for the company to a solid money loser - at a time when the railroads were least able to afford such things. So in exchange the feds agreed to directly subsidize passenger rail via Amtrak, and the railroads were removed of obligation to run passenger trains. This is the obligation at question in this case.
In any case, I dont think they owe the public something anymore because of those land grants. The debt to us from that has been long paid off.