However the Olympic marathon is special because it is completely different. In most other marathons, runners care more about their time than about winning, because it determines whether/how much they get paid to run other marathons. In the Olympics, on the other hand, nobody cares about times.
Similarly, the classical one on one match for the world championship in chess is different from tournament play. In the former, you have to beat the strongest player in the world; in the latter, you have to beat the weaker players or top players with an off day and prevent getting beaten on your off day or by stronger players.
It's the same in soccer. There, there are both national competitions where consistently beating weaker teams is the way to win and national knock out tournaments where one has to beat the best team to win.
And yes, knock out tournaments are more likely to have the weaker team win, but that can make them more attractive, as determining the strongest player may take a long time (for an example, see http://en.wikipedia.org/wiki/World_Chess_Championship_1984)
IMO, the 'only' problem with the chess world championship is that the organization is a shambles. Fix that, and nobody will complain that the knock out tournament is different from regular tournaments.