If highways weren't freeways, and if the Federal and State governments held them to financing standards similar to other public transit ...
Toll roads everywhere: automatic, electronic metering for cars and trucks. Discounts given to pre-purchase, bulk travel (interstate hauling? regular commuters? carpoolers, or those who can demonstrate that they carry three or more people from ~1 mi of origin to ~1 mi of destination?).
This would create disincentives for ad-hoc trips, perhaps, and certainly not encourage people to commute long distances for work. Exemptions for those who make under a certain amount per household? This might reduce charges of economic unfairness. Discounts for drivers with more fuel-efficient cars? This could be deeply tied to state automotive registration. Of course, data would need to be anonymized at some level, so that the government could not track movement in a scary way. Perhaps the data could be put in escrow with a trusted independent auditor or bank, in the same (shudder!) way that Verisign holds the domain registry?
Perhaps two banks or auditors.