This is caused both by supply factors and demand factors.
On the supply side, there is a higher supply of some kinds of athletes than of others. There are, for example, many more people who can play defense and rebound well enough to be run-of-the-mill power forwards in the NBA (like, say, Tory Murphy of the Lakers) than there are of really elite shooting guards like Dwyane Wade who can score, play defense, and create opportunities for others. This is one reason why Wade gets paid more than Murphy.
There is also more demand for some athletes than others. Looking at different kinds of sports, there is much more demand in the United States for football and basketball players than for soccer players. The public is much more interested in football and basketball than in soccer and therefore soccer players are paid much less.