The same reason why E-Sport and Chess have women's only leagues. One reason is to just showcase to young girls that there are female athletes in the sport. Having role models is super important for attracting new girls into the sport. And it also makes it easier to connect with other women in the sport. If they are scattered over the multitude of lower Series, there might be 1 or 2 women in a competition. This makes it very hard to build a network of people who go through the same as you.
Having a female-only competition also creates a "safer" space. The amount of hate women get is well above what young boys face. Having some female-only tournaments gives girls and women a place to compete with less discrimination.

But there are/were also some technical reasons. Most cars are built around the average male physique. And the design makes it harder for smaller drivers. Especially steering wheel size is an issue. Support series often lack power steering, and then trying to control the car with a steering wheel that is too big makes it harder. The W series has steering wheels that accommodate female drivers better. Formula 2 listened to these complaints and made some changes to the 2024 season to accommodate smaller drivers more.