It’s a fair point to bring up. An even more basic example is just the concept of female locker rooms and bathrooms, or “lactation rooms” in airports and schools. Those spaces are not created specifically with protecting women in mind, but that is still an important part of why they exist. Here is why I think those examples (and female only traincars) are ok and being able to request the gender of your driver isn’t: there is no harmed party in the above examples. If some women move to a special train car, there will be that much more space in the other train cars for men. As long as the number of female-only train cars is set properly, nobody is harmed or even slightly inconvenienced. On the other hand, if drivers cannot find work because riders are requesting only women that is clearly harmful.

I’m not sure if you are familiar with racial segregation in the United States but ultimately it was struck down by courts on the conclusion that, despite the claims of services for whites and blacks being “separate but equal”, they were in fact discriminatory against black people. Whenever you are segregating or treating genders/races differently, you have to be extremely careful that you are not harming anyone.