Pretty sure the WCML Virgin services make a huge profit, with no need for state subsidy, yes, some services take a subsidy but Virgin WCML isn't one to the best of my knowledge.
It may be profitable now but it certainly wasn't always so and I doubt the 'premium' now finally being paid to govt has yet overfed the earlier subventions. And that's just revenue, before we start on the opaque structure of both track access charges and rolling stock ownership leasing.
It would take for more time than I've got now to fish out the detail from Roger Ford's copy in Modern Railways over the years. Two pieces from newsapers a t opposite ends of the political spectrum give a flavour:
No way to run a grown-up railway - Telegraph
The truth about Richard Branson's Virgin Rail profits | Aditya Chakrabortty | Comment is free | The Guardian