Well, one school of thought is that the men do more work than the women and so deserve more, but then if that is the case I see no reason why you can't fully extend that argument and have all of the winnings fully dealt out according to time on court, or number of sets won. Does a man who takes 5 sets to win deserve more than someone who rattles of 3 quick sets? If a woman takes 3 sets to dispose of someone, does that mean she's done the same work as the man who has won in straight sets?
If it's a question of prestige, and viewing figures, then the men's tour is more popular and brings in more money, and so perhaps there is a vaild point with this kind of argument, more so than the previous.
Either way I find it hard to get very worked up about one set of millionaires earning a few more thousand than another set of millionaires.