Highways (tolls) tend to be far less profitable than rail systems (ticket sales). If the US didn't like government subsidies, we wouldn't have built all these highways.
No such fee structure could plausibly fund any rail system outside the NE Corridor. Prices adequate to sustain the network, let alone build it up, would put ridership into a death spiral.
You can't disregard the history of the highways, or the reason they were first built - for the military in the name of national security.