I think the sticking point is less where the taxes/fees are collected, and more where the money goes.

Bridge tolls, if the revenue goes strictly to operating the bridge, illustrate what's rational.

Gas taxes, as presently set up, are irrational, because the money goes mostly to the operation of conventional roads, and only a little bit toward the actual cost--that is, burden--of gasoline: Pollution cleanup. There's less proportionality (a concrete measure of "fairness")--drivers of gas-guzzlers pay more for using the same amount of road as a Prius driver.

Seems to me that a per-mile operating tax that goes to upkeep of conventional roads would rationalize the entire system. Insert three-legged stool cliche-analogy here.

Gas taxes could be directed toward pollution and climate change mitigation, bridge and ferry tolls pay for the extraordinarily expensive bits of infrastructure, and the per-mile operating tax pays for the conventional roads. In each leg of the stool, your cost is more accurately allocated. Drive a gas-guzzler and pay for the impact with higher gas taxes; use the same amount of road as a Prius and pay the same; and pay the same bridge tolls as a Prius.

Of course, a nitpicker would pick on the fact that Dan's Grand Am weighs a lot more than the Prius. Sorry, Dan, but what would further rationalize the operating tax is to base it on vehicle weight. We do that now with commercial truck fees, so there's ample precedent.

How to collect a per-mile tax? Ask the NSA for its stored GPS data lifted from cell phones and vehicle GPS units. Or put bar codes on license plates and scanners at each milepost. Easy-peasy.