In the immediate postwar era, Japan's population wasn't quite as urbanized, so the political system may not have been so weighed towards rural areas then, but over time, as more and more people moved to the cities, this changed.

The Occupation authorities felt that rural poverty was a big factor (though not the only one) which encouraged the growth of Japanese militarism. Thus, a very thorough and far-reaching land reform program was implemented. This was very effective in reducing rural poverty as well as increasing agricultural productivity. The other consequence was of course that rural voters gained real clout, and legislators of rural districts made sure that their constituents got their fair share of the gravy (and the pork) when it came to public works projects. Not surprisingly, you'll find many areas of rural Japan pretty "overbuilt" with public infrastructure that is way more than they need.