Here's a long, sometimes informative, sometimes infuriating discussion about whether female Go players are discriminated against:
http://senseis.xmp.net/?DiscriminationInGo
One argument for the persistence of women's tournaments is to "protect" them from having to compete against men. By this argument, since female Go players are rare, even the best among them are outmatched by the best male players since the latter come from a much larger talent pool.
Another line of argument concerns traditional Asian family pressures where boys are encouraged to start playing at six or seven while girls are not.
There are also some hormonal explanations, right/left brain theories, and some attempts to compare gender differences in Go to gender differences in science and math performance. Having no professional training in brain science or biochemistry, I can't comment intelligently on these arguments. As a lay person they sound remarkably sexist to me.
One female poster, "gogogirl," specifically attacks the portrayal of women in
Hikaru no Go as sexist.