NYC's highline comes to mind with talking of elevation separation. If things are truly desperate, street running track can be installed, and street running would have to be strictly limited to weeknights, and trains couldn't be more than a certain length.
IMO, when I first started this thread, I was more talking about highways/interstates that are ground-level, like the cross country behemoths like I-95. The trucking industry gets what seems like free access (or at least, very minute cost) to an important ROW, while railroads still have to pay property taxes, directly pay for maintenance, etc. on their ROW. I was implying that, if possible, the government should do one of the following:
A) Build rails in median of important highways where it is easy to do so, and charge little to nothing for railroads to use it. This gets complicated since you would need some sort of dispatch/signaling system too, but perhaps the government could require that railroads that use this track have to provide it themselves, to the government's standard. This option would also make sure that no single company can dominate the ROW's ownership, as shortlines, Class I's, Class II's, or any railroad that can afford to connect to this ROW and have pay for adequate signaling has access. This access, would of course, be "free," granted the railroads pay their other taxes (like income), are safe on the rails, and have adequate signaling/dispatch, and pay for/do basic maintenance.
B) Amtrak is always talking about new routes, but Amtrak seems to be limited to using existing freight routes not owned by them. Well, the Interstates and Amtrak are both owned by the federal government, so why not put some Amtrak routes down the medians of interstates where possible to do so somewhat easily? By doing so, Amtrak could get decent passenger numbers, since following an interstate's ROW surely means that the trains will go somewhere where people want to go. And most importantly, Amtrak will have priority on these rails, since they own them. Amtrak could also treat this like the Northeast Corridor, and charge railroads access to these median routes, being another point of revenue for Amtrak.
C) Sell the rights of medians to railroads so they can use it for ROW. The government could sell the rights of these interstate ROWs for a certain amount every 10 years. While one railroad could obviously dominate in this case, having to renew every 10 years or so ensures that there is some sort of competition for these coveted ROWs. A railroad could be outbid, or be evicted on bad behavior, with the contract being given to someone else.
Having highway ROWs into urban areas will be tricky due to the grades and what not others have mentioned here, but on the way to these urban centers, using some of what I have suggested, I think it would be a good way at making railroads competitive with trucks to/around these urban areas, so we can have less emissions and less traffic on said highways.