The "subsidy" is not straight-up tax dollars being given to Exxon & co, but computed against "prices fully reflected supply costs plus the taxes needed to reflect environmental costs and other damage, including premature deaths from air pollution".
The total includes direct subsidies, such as tax incentives that reward fossil fuel investment, exploration, and extraction in addition to indirect ones you describe.
In the US, like many countries, these are very substantial:
There’s very little federal tax, its mostly state tax (which varies).
I add the cost of “development” financing/spying/regime change as part of the cost of oil, and the U.S. pays for all of that, which is a de facto subsidy.
Long-distance rail travel seems to be fairly expensive. Is that kind of trip cheaper somewhere comparable?