These are both examples of non-proportional tax/fee structures not standing the test of time. In the case of road use - it is weight and miles that ends up being directly proportional to the cost to maintain and improve roads. At one point, it was decided that it is FAR easier to simply tax the fuel, since it was generally proportional to that - heavier vehicles and vehicles that drove more, paid more for the roads. There are also some fixed costs, that are required no matter how many miles a vehicle is driven - this is things like traffic enforcement and management, administration, etc. These 'fixed' costs are best covered by a 'fixed' fee, such as registration fees. Having these fee/tax structures balanced with the actual costs works well, and can adapt. However, approximating one based on the other means that when paradigms shift, the balance is out of whack.
In the case of vehicles, the fuel based taxes don't work right when the wear on the road is no longer proportional with the fuel use (as is the case of electric and high efficiency vehicles) - this is best fixed by doing an actual mileage tax. A mileage tax ends up being a more complicated system to manage, and that increases the per vehicle administrations costs, which means registration fees would need to increase as well.
In the case of the water bill - districts that obtained most of their operating revenue from usage charges can see serious problems when usage is significantly reduced, such as times of drought. The fix for this is higher meter fees - fixed fees paid just for being connected to the system, regardless of usage. This covers the maintenance cost of the pipes from them to you, and will be there no matter how much water you use. The problem here is people get upset when they see high meter fees, because they think 'Why do I have to pay so much when I don't even use much water'?
They are both problems that are okay for some time, because they happen to be balanced, but when something comes along and shifts things significantly (environmental pushes toward energy efficiency, the ease of self generation, population increases pushing for water conservation, etc), the balance is thrown off, and things need to be adjusted. At the end of the day, you will have to pay for the roads you drive on, the electricity that lights your home, and the water you bathe with - but the methods of paying for it can get quite erratic during upheavals like these.
