The Guardian rather jumps the shark here:
The Guardian view on rail fares: unfair Travelling by train produces benefits for everyone – less air pollution, lower greenhouse gas emissions, fewer traffic jams. Passengers should not have to pay two-thirds of the cost
Actually, a small engined car with four people in it has lower emissions, lower pollution, than four people traveling by train. So it simply isn't true that everyone benefits from more train travel.
There are indeed some truths there though. It simply would not be possible to fill and empty London each day purely by private transport: some amount of commuting public transport is going to be necessary. And there's no reason why those who benefit from that should not pay for it: as they largely do through the subsidy of London Transport paid for by Londoners.
But on the larger question of who should pay for the railways of course it should be those who use the railways that pay for it. Some City fund manager who commutes in from 50 miles outside London should not have his lifestyle choice subsidised by the rest of us. We should not be taxing the man who cycles to work at minimum wage in order to pay for wealthier people top travel longer distances.
The Guardian is, once again, forgetting that there is no magic money tree. If rail users do not pay for the railways then there is no unowned cash that can be diverted to doing so. Either the rest of us put our hands in our pockets or we don't. And why should the poor pay taxes so the middles classes can live in the greenbelt?