I think vehicle taxes should be proportional to vehicle footprint and empty weight.
Footprint because larger cars need more parking space, which is generally at a premium in cities. I get that many people need a car but we really don't need people to fight over where to cram their giant SUVs when they usually need to move one or two people and very little cargo.
Empty weight because most cars are nowhere near fully loaded most of the time. And if you spend 99% of your time driving around with one or two people plus maybe a half dozen kilos of cargo there's a big difference in road wear between a car that weighs one ton versus one that weighs two.
Wanna pay less car tax? Get yourself a kei car. Wanna drive around in a battleship with wheels? Pay up for the road wear and space you take up.
If you think that's too onerous for people in rural areas who actually do move stuff regularly you can introduce a truck rebate for vehicles registered in rural areas. (Note: This assumes a system where the car has to be registered where the owner lives.)