I've talked about this with Verbose before, actually, in our survey discussions.
I think that the brony subculture does sort of marginalize women, and I do think that at least some male fans are very sensitive about being called effeminate because they like MLP. As Verbose will tell you, he thinks (and I agree) that an unstated goal of the Brony Study was to demonstrate the "normality" of bronies, or specifically their heteronormality, through social science. Verbose and I found that the brony population, or at least the online contingent, is about 85% male, which was supported by the results of the Brony Study. We also found that the brony population is 80% heterosexual, slightly lower than the Brony Study's results. This means that, statistically speaking, the average brony online has a 65% chance of being a straight male.
65% doesn't seem like an overwhelmingly large percentage, but if the Tea Party has taught us anything, it's that numbers don't matter as long as you should loud enough. If a significant proportion of that 65% is highly concerned with people perceiving them as effeminate, then they could easily create the sort of "Brony Machismo" that we observed at Bronycon. And I think that was the case. That sort of "Brony Machismo", or internet machismo in general, or even machismo in society as a whole, really relies on the stereotypical 1950s gender roles that we see in old movies and TV shows. And I think the Daily Dot article really exhibits that; as it says, in the documentary, Neumann's contributions are passingly mentioned, but the focus is on how she supports the males in the fandom. She's shown to be validating their heteronormitivity by fulfilling the 1950s housewife archetype.
I don't think that bronies are intentionally sexist or purposefully marginalize female fans. But I do think that, since the "Brony Phenomenon" is predominantly male, women who ascribe to the MLP can feel out of place. As Zillie pointed out, the term 'brony' started as a portmanteau of /b/ and pony, but I think that it has since evolved to be more of a portmanteau of bro and pony. Thus, it is seen by most as an inherently male phenomenon. Female bronies thus are either seen as being "one of the gang", so to speak, or "not one of us". "One of the gang" can be taken in the same sense as the phrase "lady gamer"; a female who shares many interests with those of males, not necessarily masculine, but nonetheless "one of us".
And then there's "not one of us". This notion, I think, is the root of the issue many bronies have with the term 'pegasister'. I think most male bronies see a clear distinction between "female bronies" and "pegasisters"; the former are "one of the gang"-types, whereas the latter are the more typical female fans, who share an interest in MLP, but who perhaps do not share many other interests with male bronies. Pegasisters don't have to prove their masculinity because they like MLP, which runs contrary to most bronies. And since bronies are such an insular community, because of all of the outside suspicion they face (this is despite all the internal talk of "love and tolerate"), I think there's a distinct mentality of "you may like the show but you're not one of us", and I think this gets applied to the term pegasisters. Thus, pegasisters and bronies aren't seen as equals; pegasisters are outsiders.
Now I'm going to (hopefully) tie all this rambling together. One prevailing commonality between bronies is their, um, lack of life experience, so to speak. So, when this overwhelmingly male, insular subculture, obsessed with proving its own masculinity and machismo, is confronted with female fans who they don't quite see as equals or members of their society, their natural response is to apply their notions of machismo (and associated gender roles) to these female fans. Thus, many pegasisters are marginalized by the brony majority. The word 'pegasister' is hated because it describes an unequal group.
But, since the brony fandom is largely predicated on the notions of love and tolerance, these problems are largely ignored, the word 'pegasister' is shunned, and female fans of MLP are forced to choose between becoming bronies, with all the meanings and expectations that entails, or remaining outsiders. To me, it's almost the fandom's dirty secret.
This is not to say, by any means, that all bronies are like this. This is just my observation of the subculture as a whole.