I subtract all their taxes. If Exxon pays $100bn/yr in various normal taxes, and the government pays them $1bn/yr in fossil fuel subsidies, that's a net subsidy of -$99bn/yr.
How can it be a fair representation of their situation to only say they receive $1bn/yr in subsidy?
Because something like income tax is a given. We're not comparing against a world with no government. We're comparing against a situation where they get no special attention. You can use whatever word you want for it, but if a company pays half as much tax as everyone else that's a big deal.
You're right to say that it's not fair to only list the $1bn. It should be put in context of the $100bn of normal taxes. But reducing it to "$99bn" is not a fair representation either. It doesn't tell you if they otherwise would have paid 100 or 200.
How can it be a fair representation of their situation to only say they receive $1bn/yr in subsidy?