Up north here on the island of Hokkaido the roads tend to be wider and the cities smaller. I'm not sure if courteous is the term I would use, but people are generally careful to give you the room you need. In Japan, it is understood that in a motor vehicle vs. HPV or pedestrian accident, the motorist is considered in the wrong unless proven otherwise. So things are pretty good for cycling, especially here in Hokkaido, although I haven't ridden down south.
Quite a few cyclists come up to Hokkaido to tour in the summer, because it's generally cooler, less rainy and less humid than down south. I think the width of the roads has something to do with it to. Motorcyclists too, called 'riders' here, come in droves in the summer. And it's common for touring cyclists and touring motorcyclists to wave when they pass each other. It's interesting that when I go for a short ride with no panniers, almost no one waves, not even other cyclists, but when I go out with panniers I join the brotherhood of two wheels and pavement.