They should be higher, but it's all about who you play. If you get stuck in a group with low ranked teams, you have a harder time going up the rankings. Like with the USA. They've won 14 of the last 16 games, but they played teams like Jamaica(78), Cuba(84), Belize(145) and El Salvador(93) that aren't that high on the list. That said, Mexico, Costa Rica, Panama and Honduras are all in the top 40 right now. And beating Germany in that friendly was a huge boost to their score.
A lot of people hate the system they use, but I don't know of any alternatives.