Most of the major airports in France have train stations built-in. For example, you can fly to Paris airport then take a train directly to Lyon; no need to go into the center of Paris first. It’s really not much different from changing flights.
https://en.wikipedia.org/wiki/Category:Airport_railway_stati...
But I suppose the majority of overseas travelers coming into France by air with the intention of connecting to a smaller city do so via Paris or Lyon. As European travelers seem to enter by car or go directly to their destination. At least that’s my impression from reading a few articles about tourism in France.
Looks like the two Paris airports together get 10x the traffic of Nice.