Why not a national interstate rail system? Roads can still be used for flexible local transportation while railroads are used for mainline logistics and transportation of passengers.
Assuming you're talking about the USA: it's very big. No other country (except China) uses trains for US-size-wide passenger transport. Aircraft are more appropriate.
One driving factor in the creation of the interstate system was military - we wanted the ability to easily move troops/supplies across the US without airlift or rail. Not sure that's still a valid need (as in, I don't know - would need to ask a general).
Also, the US is huge. We do need some sort of road system to get across it. Building rail to everywhere is prohibitively expensive.
That said, we should/could have good high speed rail in the densest areas. Like expand the Acela corridor
tl;dr - DC-NYC tops the list (and include Philly and Balt). LA to SF is near the top. Chicago-DET-Toronto is up there. And on down the list.
Basically, there's no good reason (other than momentum/history) to not build out solid rail networks over parts of the US. I don't think anybody reasonably expects an LA-NYC link any time soon because flying is a better option for now.