A healthy living environment has value too. The point about taxing short-haul flight is that otherwise their pricing does not account for externalities that we collectively have to pay for. The absence of tax is effectively a subsidy.

Rail has several advantages, time-wise. Airports are far from city centres and security theatre takes a lot of time. Cheap flights also tend to use smaller, more remote airports because they are cheaper to use than big hubs close to large cities.