FIFA World Cup qualification is not a fair process, but in some ways it is not meant to be. The process tries to weigh bids in the finals such that the best teams in the world are represented in the tournament, not taking into account the size of a federation but rather its success at the tournament.
The journal Soccer & Society published by the Taylor & Francis Group has published an article titled "Unfair Play in World Cup Qualification?". The full text of the paper is printed here (http://www.tandfonline.com/doi/full/10.1080/.U5iuphZoIgo) with the crux of the argument taking data from the 1998-2010 World Cups to see if the current qualification process really gives the spots in the finals to the best teams in the world.
It's a rather long piece, but the stat which stuck out the most was this one: "In the 25 matches involving non-seeded teams, played outside of Europe, UEFA teams only managed to win five games.". Almost thirty percent of eligible UEFA teams qualify for the finals, but teams like Greece, Slovenia, and Scotland haven't performed at the level of their region's best.
Certainly there are questions to be asked about the nature of seeding, for example in this current World Cup Switzerland are seeded after winning a group which included Iceland and Slovenia as the next best teams. Unseeded France wear placed in a group with Spain, and unseeded Portugal saw Russia take their group by a point. To the objective observer, that doesn't make Switzerland more likely to win in Brazil than Portugal.
Still, UEFA is granted the most bids at the World Cup despite teams 10-13 performing worse than say the lowest ranking CONMEBOL team which already gets to qualify half it's membership. There's an argument to be made for CONCACAF getting another automatic bid, given the way their teams have performed in the Intercontinental Playoffs for the .5 bid teams.
Also interesting in the article is the note that countries that qualify for the World Cup are given a one-time payment of approximately $8 million as an appearance fee, which shows how qualifying for the World Cup can greatly boost a country's national team in the next cycle even if they perform poorly in the current cycle.
Club teams which have a player appear in the World Cup are given consideration based on the time played in the tournament by their players. The money allocated this year is $70 million, which is broken down to $2,800 per day for each player participating. The cycle begins two weeks before the World Cup.
So for example, if the US were to make the quarterfinals Omar Gonzalez would be worth $106,400 to the LA Galaxy; assuming MLS doesn't pool the money from all its participating teams. By cutting Landon Donovan, Jurgen Klinsmann effectively cost the Galaxy money. Drawing from MLS over players participating in Europe's lower divisions is good for the domestic league in the long run.
Part of the article's conclusion is that the United States has to increase their presence at the tournament for CONCACAF to receive more respect. The US and Mexico being respected by FIFA organizers will help the Costa Rica, Honduras and the like have an easier go in the future. If CONCACAF nations are sending their best players to MLS, that's more FIFA money in MLS' pocket. It's all connected.
There's a lot to think about in the way that the financial windfall from the world's biggest and most profitable soccer tournament trickles down. Since much of that money is from sponsors and international broadcast packages, tinkering with the system is not something to be done lightly.