Except that's not the case. Railfreight, is an entirely commercial operation, except one or two very small grants for providing freight facilities for environmental reasons that what otherwise not be commercial. They amount to a few million a year for specific capital projects.
The problem with the proposal, is one again the same is not applied to road. If you were to take the true cost of damage to the roads, a lorry causes 16,000 times (on average) more damage than a car. In an accident, an HGV causes far more damage than a car, they are also far more polluting. Is anyone seriously suggesting we hike road tax up for HGVs to reflect this?
The aim of the document is to reduce cross subsidization, yet all networks tend to have some degree of this in order to survive as a service. For example, is it not cost effective to lay water pipes to a remote house, or take post to the north of Scotland, and do remote roads really pay their way? This is effectively cross subsidization.
Likewise HGV traffic is heavily cross subsidized by motor cars. It would be unaffordable for the road haulage industry to finance and build a separate network, yet that is exactly what rail freight is expected to do.
http://www.rail-reg.gov.uk/pr13/PDF/freight-charge-consultation-may2012.pdf