If you go to the website you linked, the flash shows blue states overtaken by red all over. It's allegory for what would happen if those evil republicans had "what they really want". Considering it's a Spike Llee film, you can be certain it's racist...against anything white anyway.
Yeah, they did that in the movie too. It's funny because this movie isn't embraced by anyone. On the one hand, it can be seen as an attack against the red states. On the other hand, blue states don't want to have anything to do with this movie, as evidenced by the lack of publicity for it. If you put all politics aside, it can be a dramatic, sci-fi-ish comedy documentary. I would think that after Farenheit 9/11, the public would embrace more fake documentaries. : )