Quite simply, men are better athletes, on the whole - it's simple biology (you can always find rare outliers).
When you look at the stats, as has been mentioned, the skill level of the men in top 100 is a lot closer than that of the women. The difference in scoring average between the #1 and #100 in scoring avg. on the two tours in 2013 was as follows:
That's a 1½ stroke difference, which also explains why it's easier for a top women's golfer to dominate while it's very rare in the men's game - there simply isn't as much competition at the top. Also keep in mind that the difference in the women's game occurs on courses that are much shorter and much less penalizing than the men play on
For whatever reason, men are also better scramblers and putters at the elite level. Maybe that again goes back to biology, hand-eye-coordination, and men evolving as hunters. Who knows.
This is the part that perplexed me, but your stats on the top and the 100th player pretty much tells the tale. They just have to be better all around or they would not be in the top 100.
There was even another discussion that the top 1,000 male players are not really that much worse than the 100th player, and it takes many rounds to find the best 100.