Unless tolls are levied, there is no way to make those who use the roads more pay accordingly. Car licences and driving-permit fees do not take into account how much you drive. Fuel consumption, however, does. Every time you fill the tank, you pay for the roads you use. Even without taking into account the pollution factor, this leads to very high taxes.
Fuel taxes have yet other advantages.
They smooth out the fluctuations of prices at the pump. With a higher tax share, the wild movements of prices on world markets have less bite. Europe was much less affected in the short term than North America by the recent surge in crude oil prices, for example. And as higher fuel prices lead to less fuel consumption, foreign dependence is reduced in the long term. Sure, some people are going to be hurt by higher fuel taxes.