They don't, and most japanese roads (including highways) have ridiculously low speed limits[0], but as rangibaby notes the speed limits are uncommonly enforced, nobody respects them
[0] default 60km/h[1] for undivided inter-urban roads though it's common to get a 50 or even 40km/h speed limits, the default highway speed limit is 100km/h[2] but it's commonly lower than that, and I've seen limits as low as 70km/h on highways, keep in mind that all highways are toll roads and they're expensive as hell (entry fee of ~¥200 plus ~¥25/km[3], Hokkaido has a special tourists rental ETC[4], Honshu does not)
[1] under 40mph
[2] 62mph
[3] ~¥40/mi
[4] from ¥1800/day for 2 days to ¥800/day for 2 weeks or more, unlimited travel. With regular ETC, going from Sapporo to its airport (New Chitose) is ¥1400.
But I've heard very good things about Japan's bullet trains, so I'd guess there's lees need for highways.
In Europe only France seems to have high speed train that actually goes at high speeds. German ICE is chugging along in first gear all the time except for short stretches but those are are very few and between.
I once took Cologne to Amsterdam with ICE and it took more than 3 hours, which defeats the point of a fast train.
JR built Shinkansen-only tracks that have their own stations and no level crossings, which means they are essentially going their full speed the entire journey.
Driving is still popular here.
A) It's fun, there is a lot of beautiful scenery to admire and highway service areas have restaurants where you can eat some local food or buy souvenirs from that area.
B) It's cheaper to go by car once you have four people, even with highway fees and gas (most journeys in Japan aren't that long in terms of actual distance traveled, and normal cars are legally mandated to have very good fuel efficiency).
TBH my favorite way to travel is by highway bus. They used to really suck, but have gotten better in the last five years or so because they have a lot of competition from high-speed rail and cheap airfares. You can travel comfortably in a big seat with free wifi and power outlets very cheaply, usually less than half of the equivalent Shinkansen ticket, in exchange for the journey taking a few hours more.
[0] default 60km/h[1] for undivided inter-urban roads though it's common to get a 50 or even 40km/h speed limits, the default highway speed limit is 100km/h[2] but it's commonly lower than that, and I've seen limits as low as 70km/h on highways, keep in mind that all highways are toll roads and they're expensive as hell (entry fee of ~¥200 plus ~¥25/km[3], Hokkaido has a special tourists rental ETC[4], Honshu does not)
[1] under 40mph
[2] 62mph
[3] ~¥40/mi
[4] from ¥1800/day for 2 days to ¥800/day for 2 weeks or more, unlimited travel. With regular ETC, going from Sapporo to its airport (New Chitose) is ¥1400.