Basically, Fuji is using interpolation to up-rez their images to 12 MP. What is unique about Fuji is that they use a diagonal grid of image sensors instead of the typical row and column of most CCDs. The article elaborates on the possible advantages of diagonal sensors. On top of this Fuji applies "aggressive" interpolation (as described in the article) to arrive at a 12 MP resolution.
The article suggests that Fuji's system is able to yield slightly sharper images then competitor's images using CCDs of the same pixel count. However, the images would not be mistaken (my own editorial interpretation) for images taken with CCDs with twice the pixel count.
In other words, I take this to mean that Fuji's 12 MP images might arguably be better than Nikon's 6 MP images but you will not get a 12 MP quality image. And in fact, something like Genuine Fractals might give you just as much quality improvement. But I don't want to start that debate.