[EDIT] Incidentally, maybe we shouldn't subsidize truck shipping! But using usage taxes to pay for highways while not shifting the burden such that truck shipping is paying the lion's share of the cost and is no longer (so very much, at least) subsidized, would be making non-commercial drivers subsidize truck shipping (even more than they already are) which subsidy (to some degree) benefits everyone, including non-drivers, which seems like a weird and/or bad move to me.
Rural living would be way more expensive and inconvenient without truck shipping subsidies. Which, maybe making rural living artificially cheap is a good idea and maybe it's not, but that's one big shift that would happen if we made truck shipping pay its way entirely.
[EDIT] For true long-haul, I'm with you, the majority of that's surely only viable because of those subsidies, and we'd be better off pushing that to rail, ship, and barge.