Originally it was because it was so male dominated that having women's only tournaments gave an opportunity to grow the game among women in an environment that was less likely to drive women away. The categories aren't men and women, but rather open and women. Anyone can participate in open events.

They do things like ensure certain amounts of prize money can go to women so the game develops its player base, or avoid situations where bigotry or similar issues drive players away (safer spaces for players). Provides an opportunity for youth to see people like them being successful. These kinds of things. So there's merit to the idea, even in a game where physical differences aren't really relevant.

All of which, of course, suggests that it's a terrible decision to ban trans women from women's chess tournaments, unless of course your goal is exactly the kind of bigotry that this was originally meant to reduce.