As it happens, I was thinking more or less the same earlier today as I rode up to Earthcott Green (it's a real place!). The trouble would be setting the charge at a level that seemed reasonable to passengers and worth collecting to TOCs. What seems reasonable will vary according to journey obviously and personal perception but also, I think, train type. Paying for a space in an HST or Voyager seems, to me at least, more reasonable than in a little train with flip-up seats or a space in the corridor just because it is a proper, designated bike space. Even if it's crap, as in a Voyager.
It also occurred to me that the "ideal" might be the resurrection of something like Red Star (but with a better name) to give trains guard vans and a use for them. GWR recently started carrying fresh oysters (or some other sort of sea creature) from Cornwall to London. That service uses an HST and they still have a guard's van (and separate bike space).