I don't really think it is, and I think it's gained percieved legitimacy simply from repetition and overuse. From what I understand, "safe space" was originally an idea used in the treatment of PTSD (joke about Melody Hensley goes here), but has, from what I hear, been demonstrated to be potentially counterproductive in that context, as well.
And sure, you can have a "womens support group" or similar, with scheduled meetups in specific locales at specific times, and I wouldn't really mind something like that being women-only. But setting up a a permanent "womens-floor" or "womens-building" (womens dorms and bathrooms notwithstanding, naturally) with the motivation that maybe they want to talk about their periods doesn't seem quite kosher unless there's an equivalent for men. Or replace men/women with blacks/whites/hispanics/asians/etc or any given combination of LGBTQ people. And to have such a thing not merely being suggested or asked for, but demanded, smacks of rather spectacular entitlement.
And what of the marginalised people who won't be kept safe in a "safe space" divided along those lines? Maybe a black guy is harassing a black girl. A black-only safe space won't help then. Maybe a queer woman is stalking another woman. Women-only safe space isn't safe then. Should we divide people up by hair colour? "Gingers have no souls", "blondes are stupid" etc. That's hurtful, better make ginger-only and blonde-only floor. How many floors do we have to give out? Better make floor for aspies, left-handeds and people with glasses. Are we begining to see the problems with the idea, yet?
(sorry if my tone is getting a bit agitated, I'm nose deep in my wine glass)
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I'm bored out of my skull, let's play a different game. Let's pay a visit down below and cast the world in flame.