The entire surface of the Earth is covered by large plates. These plates are constantly moving very slowly -- an average of two inches per year. The plates are rubbing together, sinking beneath each other or moving away from each other. Over time, these movements can cause earthquakes.
The islands of Japan are located where three plates meet. Throughout history, Japan has been subject to many terrible earthquakes.
This short video has a great explanation for how earthquakes happen.
The USGS has a a website for kids about earthquakes with more videos and educational games.