I generally agree that it is better to tax emissions and let consumers decide where to spend their carbon budgets. For example, I don't support the idea that we should ban beef, because there are people who want to eat a hamburger and never burn motor fuel, and good for them.
But, in this case, that logic doesn't seem to apply. There is nothing "free market" about either air or rail travel. Both exist within and only because of the structure of government, and would not exist without regulation and subsidy.
The government of France owns a third of Air France and 10% of Airbus and half of Aéroports de Paris. I fail to see any rational reason to conclude that domestic air travel within France is "not subsidized at all".