Comparatively few people in Japan drive or even own a car, the country is too densely populated to allow for expansive car ownership and so it is discouraged. The tolls are insane on structures and bridges, I took the Tokyo Aqua-Line and paid $30 for the privilege. However, it saved me two or three hours (depending on traffic) and it was worth the money.
The Akashi Kaikyo Bridge was $20 or something, I dont remember specifically, but it also saved me two or three hours on a ferry. I didnt think the regular toll plaza rates were all that expensive. Its also hard to determine what is expensive when everything costs in the many thousands of yen, though.
The Expressways in Tokyo are awesome, they wind through skyscrapers 7 stories off the ground and have awesome views. The traffic (on the B- , C2-, and C1- at least) was never that bad for it being the largest city on earth.
There are some Japan blog posts at blog.aaroads.com. Also, most of Tokyo and Osaka's Expressways are on Google Street View now.