Right, the externalities of those road systems aren't really paid for properly, by anyone.
But that's hard to do, because for many people/uses, they have to use those roads to get done what they need to do. The alternatives (like high speed rail) just largely don't exist in the US, or are painfully sub-par.
We have to distinguish between several levels of externalities and between different timespans.
About the former: when you drive on the road, you cause congestion for other road users. But having the roads at all (and having them used) also causes externalities for others, who ain't on the road. Like cutting up nature or noise.
About the timespans:
In the very short term, demand for specific roads is inelastic: if you live in one place and work in another, you have to commute.
But over several years demand for specific roads is very elastic: people and jobs can and do move.