Why don't the trains just stop doing the empty runs on the outlying routes, then?
Because trains are considered an essential public service.
The people with only outlying routes nearby would be stuck without public transport, which is unacceptable. Commercial train companies only get contracts for the busy intercity routes if they also provide service on the outlying routes.
It makes flying seem more competitive then it actually is, as trains usually aren't booked relative how much your transportation cost and instead the overall cost to also enable these almost empty routine runs