If the answer is "Men cannot understand" that's fair, but a terrible simplification. You'll find most men are at least willing to try to understand, and by vilifying the majority and hiding in a smaller exclusionary group you may just end up worse off than before.
To me, as a member of this minority group, I see this service as offering a solution to one aspect of (but obviously not the entire) problem: that of community and validation. A de facto understanding based on shared experiences. It does not mean that men can't understand and can't help, but that comes later or alongside this component of building strength in numbers.
If you are the only woman on a dev team, for example, who at work can you talk to openly about your experiences without fear of judgment/professional repercussion? We've seen what HR is (in)capable of in stories like what surfaced at Uber. And the men on your team may be the most emotionally intelligent, compassionate beings but they still won't be able to fully empathize. Maybe they will say, "I hear you, and I think that is awful, so what can I do to help?" (which IMO is a wonderful response), but they likely can't say, "I know exactly what you mean."
I hope people don't see Leap as a vilification of the majority. I have signed up for the beta but haven't used it yet, so I don't actually know what the overall culture is like. I sincerely doubt it was anyone's intent to alienate men, but rather to create a safer space for women than the tech world at large generally provides.
ETA: To address your point about a men's group--you're right that it probably wouldn't be received well, which isn't fair. But it also wouldn't be getting much of my sympathies, as its need for existence is altogether different.