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For the most part, basing tax on gallons purchased is a reasonable surrogate for a miles-driven basis ... close enough that spending millions of our dollars to get questionably closer is not where tax revenue should be spent. As far as losing money because of electric car usage; seems someone should have thought of that before they seduced the uninformed (with our money again) into using this technology.
I thought the whole idea behind tax-funded incentives was to "bite the bullet" whilst encouraging early adopters into promising new technologies. Promising in this case meaning properly researched technologies with clearly defined timelines for incentive payback and long-term profitability. Crying about loss of tax revenue at this early stage is worrying but not surprising.