A per mile fuel tax just doesn't make sense. It would be too expensive. A new government infrastructure would have to be created just to monitor people's mileage and bill the tax. Even though the article claims the fuel tax is not working because fuel consumption is down due to vehicles being more efficient, raising fuel taxes would be much a more efficent way to recover the loss in tax revenue than creating another inefficient beauracracy to track mileage and collect the mileage tax. The argument that increasing fuel price by increasing fuel taxes would discourage people from traveling as much, thus further reducing the amount of tax collected, doesn't really apply here since a mileage tax would have the same effect.
One could argue a higher fuel tax is unfair because vehicles that use more fuel per mile would have to pay more taxes. However, that argument would hold little water because the reason most vehicles use more fuel is because they are heavier which causes more wear and tear on the roads. In the case of diesels, fuel taxes are already tiered by weight. Diesel fuel at passenger pumps in many States (AZ is one) is taxed differently from the fuel pumped at the big rig pumps, usually based on the number of axles and overall weight.
All electric vehicles could have a flat tax added to annual registration fees to recover revenue lost because they do not pay fuel taxes. Or, in States that already have an annual inspection for emissions or safety could require all electric vehicles to also be inspected to monitor mileage and report the mileage to the taxing agencies. Very little added infrastructure would be needed to administer the tax, mostly improved computer programming.