This is how I interpret it too. It's self-deprecating and ironic. It is a complex reference though, so its not surprising that some people misinterpret it.
FWIW, I think brogramming is self-deprecating and ironic too, and not the least bit offensive. But Tess doesn't - and I respect that.
EDIT: You're not obligated to stop doing something simply because somebody thinks it's offensive. But it's kind of the polite thing to do.
But there are a large number of women who DO feel that it's offensive. And I cede to them. (Which is what Alexey's getting at.)
Here, my common goal with the OP is that everybody who wants to program for a living feel welcome to do so. As a well-off white male, there's very little people can say to offend me. (Which reminds me of Louis CK's great take on this: http://www.youtube.com/watch?v=TG4f9zR5yzY ) But that's not true for everybody, and I'd like to make sure that everybody feels welcome and safe in my office and in my field.
So whether or not I'm personally bothered by the brogrammer stuff, I think it's reasonable to honor the suggestion that it not be used in situations, like recruiting, that will make some people feel uncomfortable.
There's also another dimension here: describing yourself as a brogrammer vs creating a brogrammer atmosphere. I don't think the term brogrammer itself is offensive such that it entails purging it from our lingo. It's when you create exclusionary groups with the term that creates the problem. Describing oneself as a brogrammer shouldn't be seen as offensive, as it's simply describing a mentality you have (perhaps as a joke, or maybe even seriously). So I disagree with the article that we should completely remove the term. It seems to mirror the effort I've seen talked about to make CS less "nerdy" to appeal to a wider audience (as if removing star wars posters from the CS lounge will attract more students). But using the term as a recruiting tool or to create a meetup centered around "brogrammer" themes shouldn't happen, as its needlessly exclusionary.