Fuel taxes, sales taxes, and usage fees (tolls) generate roughly $150 billion per year.
Excise taxes do not even have a good national accounting system and I can’t find a US total number. But, for example, just CA generates roughly $10 billion in revenue from these fees.
Far from not covering the costs, the direct taxes and fees on cars are actually generating a profit.
If you want to talk about externalities you have to account for both positive and negative externalities.
[1] - https://www.urban.org/policy-centers/cross-center-initiative...