I believe the only TOCs which actually don't require a net subsidy, once you include Network Rail's enormous subsidy, are VTEC and SWR. However, at least the former we know is (was) simply being propped up financially by its owner, with the real level of premiums that could sustainably be returned to the DfT being significantly less.
The reality is that the railway can't, as a net, be financially independent. That would require significant fare increases, or perhaps the abolition of yet more cheap fares (e.g. Advances, CDRs). Until it's financially independent it will always be in the control of the purse-string holders.