Why not dispute their findings not their funding?
Their problem is in the article itself:
"If we look at the total cost of driving, including vehicle costs, cost recovery will tend to be closer to 100 per cent."
That is true for cycling as well. If you include the cost of the bike, bicycle related clothing, etc. then the cost recovery ratio is quite high.
They also do not consider anything except direct costs. They note that money goes into general revenues but do not consider the ambulance/healthcare, police (OPP), etc. services which come out of general revenues; nor indirect subsidies like oil and vehicle manufacturing tax breaks.
Yes, fuel taxes are high enough to pay for maintenance of provincial highways. I don't think this has ever been in debate.
The second major issue is the fees are to enable drivers to move more freely on the highway. It's the "I want to drive faster! Too many cars in my way!" fee. Raising the cost will decrease congestion along those routes with the increased fees as will providing alternatives.
If drivers want to have a 2 hour evening commute home in a decade; so be it. If they don't, then they need to look at reducing their numbers. Making it illegal for even numbered plates to drive on odd numbered days is another way of doing it (forced carpooling).