Besides watching a lot of documentaries and South Park, I also watch a lot Japanese films and animes. One thing that I have noticed in the films/animes is that Americans are often the villain. The most recent film of this genre, in which the example is very obvious, is called "The Host" (Gwoemul), directed by Joon-ho Bong. It is technically categorized as a horror film; however, I would consider it more of a creature flick, it wasn't really scary at all--hardly even gory.
Interestingly enough, it was the actions of uncaring American doctor that allowed the creation of creature to take place, which the set the action of the film into motion. There is also another different slightly crazy American doctor later in the film who nearly lobotomizes the hero, who is trying to save his daughter. In other words, the Americans aren't looking so good in this film. Of course, you could say it could just be this particular film--and I would agree if I haven't seen this stereotypical "evil" American theme run throughout other Japanese work.
Although, I don't have much to base this on, I would guess that this theme has to do with the bombing of Hiroshima and Nagasaki, and how devastating that was for Japan.