There are proposals to tax cars by mileage driven rather than (cents) per gallon of gas. Still, alternative fuels like E85 (ethanol) and B20 (biodiesel) can easily be taxed just like gasoline is, at whatever rate (and thus resulting revenue) the states and Congress see fit. Electricity can of course be taxed also, but its more difficult if you want to differentiate between taxing 'energy' going into your automobile and the same energy used to run your toaster.
A bigger and more immediate differene may ber made not be alternative fuels but simply by more fuel efficient vehicles, which use less fuel to travel the same mileage as before, thus lowering the revenue collected (unless the taxe rate is raised, not a popular move). Revenue collected from the tax on gasoline has long been woefully inadequate to meet the needs of the nations crumbling transportation infrastructure.