That would essentially be a bung to the freight companies, and I wouldn't put it past them to keep producing "analysis" that shows that they need more money to offset their loss of profits. It might also have the effect of pushing some long-distance freight onto the highway.
To be honest there's probably little that can be done about the long-distance Amtraks, other than ensuring they have the resources they need - which after years of cuts I suspect they haven't. While attractive to enthusiast visitors and transport lifelines to some communities, they don't count for much in the big piture.
The big opportunities are building some of the "commuter rail" services that just provide a handful of trains in the peaktime up to something we would recognize as a European regional service, and looking at high-speed over somewhat longer distances where rail could achieve a journey time of 3hr or so to be time-competitive with road and air. Although America has lots of empty space there are some clusters of big cities that could allow this, such as around the Great Lakes and expanding the one line under construction in California. There's also the more urgent project to replace the Hudson tunnels so as to assure the future of the Northeast corridor.