The problem is that steel-wheel-on-steel-rail systems simply aren't fast enough to break flights on these long journeys.
I know people laugh at it, but if you want to kill continental scale air travel you need something resembling the Chūō Shinkansen.
It's rated to accelerate significantly faster than a tube train and keep that up almost all the way to 505km/h.
A steel rail system that struggles to operate economically above 350km/h and takes ages to accelerate there simply can't compete with planes that can do treble that.
TBH, I'm only really talking about point to point routes where there is an already existing train service which takes ~3 hours or less like Zurich-Milan, Rome-Milan, Tokyo-Osaka* etc where the train is viable.
*Yes I know the Shinkansen is rather expensive for Japanese citizens. I don't know if the Chuo Shinkansen could help reduce prices on the existing Shinkansen. I can understand why Tokyo-Fukuoka is the joint busiest domestic air route in Japan as it still takes 5 hours on Nozomi Shinkansen and is the same distance as London-John o' Groats.