The official method for ranking can be found at:
http://www.fifa.com/documents/fifa/events/FinalDraw_Pot1.pdf The quick and easy answer as to why Mexico is seeded and the US is not goes back to the 32nd place finish at the 1998 World Cup. That cost a lot of points in the FIFA system. Mexico finished 13th then. Also, Mexico has been consistently ranked in the World Rankings as a few places higher than the US.
It's not actually Mexico that was our competition for seeding, but Argentina and Italy, who each finished with one point higher than the US in the seeding algorithm. Mexico was four points above the US.
I'm sure that if the US was seeded, and Italy or Argentina were not, there would be a lot of interesting discussion on Italian or Argentinian message boards...
[Post Edit]: If you look closely, there are some errors in the points attributed to Italy and the US in the row for FIFA World Ranking. It doesn't amount to enough to change the overall classification, but it does shake my confidence in FIFA. Plus, it makes for a good conspiracy theory.
[Post Edit Part Deux]: Nevermind. There are no errors, it's just that the algorithm was not explained simply enough for my over-taxed noggin.
