Plus it completely ignores any non-highway driving subsidies, like tax revenue going to local roads and public parking areas, government regulations that mandate parking minimums, etc.
AND it ignores how valuable the land is that roads exist on, that could potentially be used for something else. Now obviously we do have to set aside some land for transportation purposes, but with cars, you have to set aside a lot MORE land, so you have to factor in that subsidy as well. E.g. if the city could, by switching to denser transportation modes, lease out a bunch of land to private companies and earn a million dollars a year, then that's a million dollar a year subsidy.
Must also factor in the untold billions used by the military to ensure cheap oil.