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...
[1] https://en.wikipedia.org/wiki/Externalities_of_automobiles Extremely conservative list on Wikipedia. Anyone that e.g. has looked at real-estate pricing before and after a street was made car free and has seen valuations go up by x2-x5 can attest even just the impact on direct livability.