Those charges will be for things like maintenance costs and to pay the leaseholder rent too.
Even if Nexus manage a station, they don't necessarily own it - so any money they do take, will be poured back into the landowners/leaseholders pockets.

I'd imagine the likes of Four Lane Ends and Heworth are owned by Nexus, judging by the infrastructure and facilities - compared to Gateshead or Park Lane, which are possibly just managed by them.

Obviously this doesn't help us passengers, who are likely to feel the burden of these costs in our fares.