Trains are limited onto tracks and cannot merge out of the way, so point to point more quickly exhausts route capacity. Stations are less of a constraint.

Trains also lower the cost of transferring; airplane transferring is at best a hassle and at worst an ordeal. Meanwhile, trains can literally stop across the same platform across from each other so you walk a few meters at most. Japan does this a lot, where trains are timed to facilitate such quick connections.