There is an interesting article here (see link below) about how they decide the FIFA rakings and World Cup seedings.
It is also interesting to note in that article that depending on WHO you play in friendlies could have a big impact on your FIFA ranking (and if you are seeded).
If you play say Germany or Spain in a friendly and beat them you get so many ranking points (and because those teams are ranked high the ranking points you get are quite good)
But if you play a very poor team in a friendly (even if you beat them) you get very few ranking points.
And if you don't get many ranking points in a match it takes you yearly AVERAGE ranking points down a bit, taking you further down the FIFA ranking table.
As it says in that article, if Holland HAD NOT played Indonesia in a friendly they WOULD have been one of the seeded team in the World Cup.
It also says if England had "managed" their friendlies better (make them unofficial friendlies) we could have been one of the seeded teams.
http://www.bbc.co.uk/news/magazine-25134584