I think the article conflated brogramming and misogyny in Silicon Valley. The former isn't necessarily bad as could be seen in the hilarious Twilio presentation.
Misogyny is not funny, and it wasn't a part of the Twilio joke - at what I recall of it - as most of it focused on what makes for an annoying programmer. Some misogynists have appropriated the brogramming meme, but it is not an excuse for misogyny. Misogyny is not funny, regardless what the pretense of it is.
"It's just a joke" is straight out of the misogyny flow chart. People are doing "more productive things than being offended" by writing this article and discussing the topic maturely in the comments in places like Hacker News.