That would be a germane and critically relevant point were anyone proposing making roads disappear. Since nobody has, it isn't. The benefits of moving people and goods is not the exclusive preserve of motor vehicles. You're barking at the moon. Calling for motoring to be taxed has nothing to do with making roads disappear. Roads will not disappear. Nobody's saying roads will disappear, so stop banging on about roads disappearing.
Your argument - roads are subsidised because they cost more than is generated via road tax, VAT on car sales and a few other 'motoring-related' income streams
My arguments - 'the motor industry' provides more income for government than you credit it for - for example the income tax paid by all the people employed by it, the tax paid by people who work for oil companies, the tax paid by employees of road bulding companies and so on.
Furthermore, the roads themselves, once built, are of benefit to the economy (which one can get some idea of by doing a *thought experiment* of what might happen if they all magically disappeared) - the document you linked to doesn't seem to give any credit for this. I imagine most companies dealing in physical goods would struggle to survive without roads, and thus one can argue that they are fundamental to the whole economy.
Essentially I am saying that the idea that roads are 'subsidised' is only true if you ignore the value of the benefits they bring and also ignore income from all the associated industries, which to me seems a very one-eyed way of making the calculation.