it's the passenger journey data overlaid on the map of tracks, where the thickness is number of journeys.
so drilling into a station like EXD (Exeter St David's) shows lines going to Aberdeen... there is no route between Exeter and Aberdeen, this is just a journey involving multiple changes.
so what you're seeing for a station is where people travel to, and the volume of journeys on those segments of line, given the station as a starting point.
I couldn't trivially determine whether it reflects all through journeys for a station (start point, destination point, stop on an through journey), it may well do so.