You can find a ticket from Madrid to Paris taking 10.5 hours for 226 EUR.
This also ignores the speed: if the prices were the other way around, with airfare twice as expensive as rail, I expect most people would still take the plane.
Airlines also typically charge for luggage, RyanAir charge extra for anything they can think of, including choosing a seat, and people booking at shorter notice subsidise those who book in advance. The cost difference for most passengers is probably smaller.
10.5 hours is still longer than 2.5 (or maybe - if you include security checkpoint time - 3.5 hours) by plane.
Also, and this may be related to the airports I fly out of, but I have hardly ever had planned more than an hour of time from entering an airport terminal to the gate. In TXL (sadly closed now for the much inferior BER), I averaged 25 minutes. At Stuttgart, I once managed to get there in 20. It all comes down to being prepared for security, knowing which security controls are often underused and picking up the right departure times. rel: https://www.youtube.com/watch?v=cnNyUGhXTsw
This is the saddest part of flying, that it really can take only 20 minutes, and instead of making it as efficient as possible, there's the opposite development, where the recommended time has gone from 1 hour to now at least two hours.