The bigger the engine, the higher your yearly car tax, and the higher your twice yearly car-inspection fee.  These are not trivial taxes.  I pay 35000 yen a year or so in car taxes for my small 4-cylinder engine, around 1300 cc or so.  Above 1450 cc you end up in a different tax bracket, and have to pay somewhere around 100000 yen a year in car taxes.  And there are even higher brackets as well.

On the other hand, if you're willing to put up with a truly tiny car and an engine no larger than 500 cc, there's a special Keizai-kuruma bracket, with negligable car taxes.

Sadly, those k-cars are increasingly replacing bicycle use, as the younger generations are too lazy to ride anywhere, and as the suburban and rural infrastructure has been optimized for car usage along American lines.