Unless "out of France" simply means originating in France, regardless of whether the destination is in France or not.
Either way, the original title is better, I would keep it: "France to tax flights from its airports"
I read that as most flights in or out of France being taxed.
"Transit flights" Is that a connecting flight? Seems to be the only exception.
Makes sense, economically, in that there is quite fierce competition between CDG and other major European hub airports for filling spare intercontinental capacity and multi-hop connections are far more price sensitive than direct flights. If CDG would lose a majority of regional (but still international) feeder traffic to FRA or AMS, Paris would experience a noticeable drop in direct connections.
According to Wikipedia (en. and de.), the French state has been divesting from air France quite a bit while the Netherlands, who had very little at the time of the merger, are about to match their government stake to parity (but both will remain at <30% combined). I'd assume that French leadership is quite aware of the risk of Air France KLM effectively becoming KLM Air France if they push too hard.