That's the thing, even putting it in this terms, doesn't seem to be some sort of anti male message, like, Joe was a shitty tyrant who deserved being taken off, it's not like they took him down cause "boo the patriarchy, boo!"
More like "Boo the toxic masculinity, boo!" And patriarchy too, I guess.
Patriarchy is a system where the men are the heads of any system of power by virtue of their being male. Joe ran an extreme patriarchy. Presumably, the wives and Furiosa will be put in positions of power. I'm sure there will be men in positions of power as well, Joe's patriarchy IS the system being taken down here.
It's not anti-man, but it is saying a system where only men have say in power is wrong.