I'm not well familiar with it, so might I ask if the Female Founders Conference is strictly limited in admission to women only? If so, your analogy doesn't pan out.
Although there isn't anything that says whether or not it's women only, the application[1] has a gender option, so at the very least they are accepting applications from men. There isn't any language that says they are explicitly excluding men, although I'm sure they'd like a more balanced ratio than other startup events, and it's likely that the majority of the attendees will be women.
To draw a parallel in an industry that went though this process some time ago, in Australia journalism was a male dominated industry and they organised programs to encourage women to enter the industry. Things like the women in journalism awards and press club events aimed at women. In the most recent one they announced the statistic that 65% of journalists in Australia are now women despite this the female targeted events continue.
Once you have these events its hard to give them up and if someone was to now organised similar events aimed at the minority group men the reaction would be very hostile.