Anyone that understands the research methodology used in the report can tell you it's pretty ridiculous to draw the conclusions published in the media. It basically says that:
"Drivers pay a significant share of the money that would be required to pay for the roads they use, to the federal and provincial governments."
In other words, the roads that they don't use but they have access to do not count. It's like saying that my transit costs involve sending two streetcars a day up and down Spadina. In reality in order for this service to be useful to me, it needs to be running constantly, and road maintenance and construction need to go far beyond what each individual actually uses on average in order to be useful. Much as empty buses - often a necessity - don't pay for themselves, neither do empty streets. When they don't include the costs of cars, and use real expenses in their analysis of Ontario, you can see that driving is still heavily subsidised.
They do fix this for the GTHA calculations (relying on the only reasonable approach to calculate infrastructure costs), but these calculations fall short of any legitimacy as externalities are not included. Although the article pays lip service to a few of these externalities, it fails to include any of them in their analysis and calculations - such as deaths, air pollution in urban areas, congestion, the extremely inefficient use of public space, etc. It's like calculating the costs of smoking without accounting for any healthcare considerations. It therefore fails to account for the undeniable fact that provincial gas taxes should actually be spent in areas other than infrastructure. In other words, the 'costs' in the article don't reflect real costs in any way.
Then there's the question of who these drivers are paying this money to. Is it the municipal governments? Responsible for actually fixing the majority of roads - and pretty much all roads shared with other modes of transport? Nope. Most of what drivers pay goes elsewhere... which means that, at the municipal level, drivers remain highly subsidised compared to other forms of transportation.
Including all costs of driving in the section of the article that looks at total costs was a pretty silly thing to do in the context of their arguments. Concluding that most externalities should be solved through the use of general revenue since people spend so much in car-related stuff is completely absurd and illogical. They can't go there without even contemplating the social consequences of having transportation costs of $10,000 per household per year, for example, and of spreading out cities to serve the car. The paper does not examine or even entertain the possibility that spending money from drivers (both in special taxes and general revenues) to subsidise public transportation might actually be making the life of drivers much easier than if the money was spent in some generic road infrastructure improvement. It also does not engage in more complex but undeniable issues such as the fact that a lot of the transit service in our cities is necessary to make up for the deficiencies of cities planned for the car: I had to take 2 buses to get to a grocery store when I lived in Mississauga, for example, but if the city had not been designed for cars I could have walked and saved us all some money.
All in all the paper does not address the real issues associated with driving in urban areas like Toronto. It merely shows that drivers in the GTA are paying money to the federal government that they never see again, and that they are helping the province pay for heavy-duty transport costs more than other user sub-groups. It does not change the reality that car-infrastructure is heavily subsidised at both the provincial and municipal level, or that planning for cars is often the least efficient form of moving people from a fiscal, social, and spatial perspective.