It's not remotely fair, but that doesn't make it untrue. Just ask the diet pill company from the early 1980s that used to advertise "Ayds helps you control your appetite so you lose weight!" Or the many Hindus today who are frustrated that their Swastika earrings get mistaken for an endorsement of Nazism.
Bro culture in tech is a poison, and one of the many crappy things about poison is its tendency to contaminate otherwise harmless things that happen to be nearby.
If you can, I'll take your argument seriously (although, fair warning, I'll take it seriously long enough to beat it to death with a shovel).
Edit: I'm going to leave that typo as is.
I can see at least two very sensible ways in which the concern that I've shared here could be unimportant (and you may see others). I don't even know enough to know to what degree either applies here.
One might be if nobody but an established specialist in the field would ever have a need to assess, use, or contribute to Bro or its competitors. In that case, the negative associations with the name would be unimportant: the specialists would be fully invested in the technical details, and the name wouldn't have any substantial exposure to the broader tech community. (The only cost would be occasional unimportant dust-ups when that exposure happens, as in this case.)
Another might be if there is a good chance that the importance of this project will outlast the public prominence of bro culture in tech. (Given the longevity of Bro to date and the promising backlash against bro culture, that seems quite plausible.) In that case, it might be entirely sensible to just weather the current storm of negative associations and trust that everyone will have forgotten brogrammers in five years. (That's only fully applicable if they really are forgotten, though, rather than being a lingering negative memory.)
You may have other reasonable arguments for setting aside the concerns that I've raised as well. But I do think that occasional undeserved distractions because of the name are inevitable, and I could imagine them being a real problem.
Have you considered the possibility that you're being that distraction and creating that problem?
Go watch a couple of the developers talk about Bro on FLOSS weekly a few weeks ago here: http://twit.tv/show/floss-weekly/296
In short, they acknowledge the possible confusion but honestly I think we are getting way too hypersensitive here in America.
Out of curiosity, if everyone saying the word Bro has a negative connotation could state where they are I have a suspicion this is a predominately California thing.
If we keep treating words with such distaste we are basically just practicing a form of newspeak or censorship. Is it possibly deserved? Maybe, but I think we are overreacting here to be honest.
This is an OLD project, saying it should change just to appease the pathos of certain programming communities seems premature.