You are assuming that the only alternative to a plane is a car. In France you also have the option to use the train. The TGV is much faster than a car. Everything considered (check-in, security, pre-boarding time) a domestic flight in France may not be any faster than taking a trip with the TGV, in fact the TGV may very well be the faster option.
Trains are stupidly expensive. I could buy 2 hour flight tickets for 15 EUR two years ago. A ticket from Amsterdam to Brussels ( 2 hours, 200KM) is 39 EUR the cheapest. It's not going to be any better, because railway companies have practically zero incentive to get more passengers.
There are many variables that affect the total cost (which includes traveling to- and from the airport or train station) such as where you depart from and your destination and date/time. Sometimes a flight is cheaper, sometimes the train.
A 747-800 uses less than 2KG fuel per passenger per 100KM. You need a Toyota Prius with 2-3 people to be more economic than the plane.
That kind of per passenger fuel consumption is only that low when a 747-800 is well filled with passengers. For short domestic flights typically they don't use a 747-800 (or other aircraft with comparable capacity), can you guess why?
Comparing a 747-800 with a Toyota Prius is rather silly, considering that routes for which a 747-800 is a logical choice a Toyota Prius is not an realistic alternative and vise versa.
France is clearly wrong here. The future is more airports, more aircrafts, smaller aircrafts, turboprop planes and going forward, not backwards. Why would you ever take a bus if you could fly?
Maybe because a bus is for short trips faster, cheaper and/or more convenient (BTW a train is not a bus, those are quite different modes of transportation). Or would you take a plane for a 50 km trip? Traveling to- and from the airports would probably take more time for most people. Add to that the time and inconvenience of security checks, check-in...etc. and the plane is not all that attractive for short distances. And all that is assuming you can get airports that close together - economics, noise regulations and safety concerns may make your dream rather infeasible.
The past decade I have traveled more by airplane than by train or bus, but the reason for doing so is mainly because the nature of these (long distance) trips.
The best mode of transportation depends on the distance traveled and the transportation infrastructure. For short distances a car or bus is usually the best option. For medium distances the choice is between a (high-speed) train or plane. For intercontinental trips an airplane is the only realistic choice.
In case of France the TGV can be a reasonable alternative for a domestic flight when you consider the door-to-door travel time. Considering the CO2 emission targets most countries committed to, and considering that in France most electricity is generated by nuclear power stations, it doesn't seem to be totally insane for them to promote the train at the expense of short flights. However the biggest downside I see is that by forbidding short flights it takes away competition from the train, which almost inevitably leads to higher prices and poorer service.