Don't forget those numbers are the reported statistics. Japan sort of has an elephant in the room approach to all things sex. I've only talked to two Japanese women about the topic, but they both had stories and knew several other women who experienced some sort of sexual abuse (mostly groping on a subway). I don't know how that translates into complete rape, but I would image the real numbers behind this sort of thing are underrepresented for Japan. Conversely, the top countries there are all pretty women sexually to differing degrees. I imagine sexual abuse gets reported a lot more there.
Now, the trick is if you can correlate rape with the mass use of games and media like this is another trick. Who knows really and it is strange that CNN is picking up on this now. The fact that there's a sizable market for this sort of thing makes me leery of Japanese culture, but I can say one causes the other. Odds are we're just seeing two symptoms of the same problem.