If an organization does a meeting called, like, "Job resources for ex-convicts", we don't get mad because what about all the people who aren't ex-convicts. If an organization does a meeting called, like, "Putting your life together after divorce", we don't get mad because what about all the people who are happily married but still need to put their life together. If an organization does a meeting called "Issues facing women in tech", we don't get mad because "what about the issues facing men in tech, like when you and your pair programming buddy wear the same j crew gingham check shirt to the dave matthews band concert". It's also okay for there to be a Black History Month.
The reason "Separate and (un)Equal" is unjust is not because it is inherently wrong for there to be a space, a place, a time, a process, or a thing that applies to one group versus another, it's because it was part of a systematic process of the state using its force to dehumanize, denigrate, and criminalize the existence of millions of people because of their skin colour.
I agree that public accommodations should be inclusive. The question is how to we make them inclusive. And sometimes the answer might involve something with a little more finesse than "Everyone Is Welcome" -- sometimes the answer does involve thinking about how each group might have different needs that can be catered to in different ways. And again, this isn't a case where we're talking about you or me or anyone getting less, it's not like there's going to be a long line of men waiting because all the unisex showings of Wonder Woman are sold out and the women-only showings, which have space, won't admit them. It's meant to be an option on top of all the showings that already exist.
I should also say btw that it's not like they were addressing a Great Moral Injustice. Like, it's a comic book movie, and many women do attend them regardless. It's more like they thought "Hey, wouldn't there be a neat vibe if the audience were all women and the showing was explicitly themed around female empowerment". It's extremely low stakes. So as unusual as the showing is, it's also, like, ... this is not a Normandy Beach for a new Matriarchal Society where Western Values and Masculinity is Punished by Feminist SJW Mainstream Media Fake News or whatever.