In my view this demonstrates why we should attempt to make all rail journeys competitive with car travel. At least in the case of one person travelling alone, which is not very efficient in the average car. A generalised cost figure should be used, not just the cost of fuel.
Of course this would require a major shift in public policy - huge expansions in railway capacity over and above what has already been committed and the money to pay for it coming from the government. There would still be lots of journeys where rail could not compete with the private car on both cost and convenience, but there would be far more than now if fares were lower and capacity much greater. Advance tickets, poor connections and infrequent services do not compete with cars. Fast, flexible (i.e. frequent) journeys in comfort and usually on direct trains are what competes.
To the OP, for what it's worth, the Super Off-Peak Return fare of £116.90 is not terrible value as it can be purchased immediately before boarding the train, leaving you flexibility to cancel or change your trip, it includes both ways a journey on London Undgerground to cross London, it's highly flexible, you may break your journey, there are no restrictions on Tonbridge - London trains, you can refund it for only a £10 charge, a seat reservation is available for free with it, the journey times are competitive (lots of fast London to York trains) and you can often change between trains in London far more quickly than the booking engine will tell you.
I appreciate that even all of this may not be enough to justify spending £116.90 - I certainly would not buy that fare. But it is worth considering that it's one of the better deals as rail tickets go. Very very hard to see how it's going to be a better deal than going by car though!
It is worth noting that if Manchester were your destination rather than York (and that is almost as far and has a similar service) then the equivalent fare is only £92.60. And at least you are not going to Darlington, where the fare is £139.10