"Brony" is obviously a combination of "bro" and "pony" but (and I admit this is kind of debatable) the "bro" part didn't refer to the sex of the fan, it was a mocking of frat boys and douche bags that use "bro" in the same way someone would say "buddy" "pal" "dude" "nigga" or whatever. It had something to do with /v/'s overuse of the word "bro" at the time (kind of like their overuse of the word "autism" now) with shit like "brolicious" "broseidon, god of the brocean" and "bro-op," it's the exact same concept used for "brony," the main difference being that there's a lot more focus on your gender when watching the newest edition of my little pony subtitled "friendship is magic" so misinterpretation was more likely.
What "brony" means now is totally up in the air, mostly regarding gender issues, the cons of labeling someone as a brony, the amount of obsession someone needs to have with the fanbase or the show to be a brony and fuck knows what else, I don't give a shit. The multitude of definitions people give it are part of the reason I personally never attached myself to the word. And obviously there's the stigma of being associated with people like the ones featured on the mylittlespaghetti youtube channel or everyone on Equestriadaily.
Also, a lot of the people in the first threads were women. GO FIGURE. WOMEN WATCHING MLP. HAHAHAHA