That flywheel was just for short uses, as I said for higher-density devices, gyroscopic forces could be a huge barrier to their use considering trains tend to accelerate in more than one plane. It's not unreasonable to assume some super-flywheel capable of powering a train for a decent amount of time would be more than capable of throwing it off the rails as soon as it hits a small dip in the rails.
Of course, it would be theoretically possible to negate such problems with sort of gimbal system, but being able to transfer the energy effectively would pose some challenges. And then it comes back to size/weight/cost.
Even in stationary installations, huge flywheels have to be installed taking into account the Earth's rotation so as to avoid unnecessary friction.