Women are permitted to ride in any car, but there are cars designated for women only. It used to be the first car of the train, but now the women's only cars are towards the back. You can find the women's car by looking for the signs (see photo on right) on the platform. The women's cars will stop adjacent to these signs. I prefer not to use the women's cars during rush hour because they tend to get more crowded. I personally have never had any problem at all riding the train. It can get pretty crowded at times so be prepared to push and shove your way through the crowd trying to get on. Not all the cars are air-conditioned and some have fans mounted on the walls, but they don't always work. For the money, the Metro is still one of the best, and fastest ways to get around Cairo.
In this video I was riding in one of the women's only cars: