Where I live, and I believe many other European countries as well, diesel is about 5-10% cheaper than gasoline (due to less tax). OTOH there's a yearly fixed tax for diesel cars (some hundreds of EUR).

So the intent at least originally was to discourage the plebs from buying diesel cars, whereas those that used a lot like trucks, taxis etc. got cheaper fuel (for them the fixed yearly tax was a trivial cost compared to the advantage of cheaper fuel and a more efficient engine).

I agree this is a mistake that should be rectified, but it is of course politically very difficult.