In general the problem is more with the atmosphere in threads that aren't explicitly about gender. This means things like the language that people use or the assumptions that they make when writing a comment. Sometimes these aren't very welcoming to women (other groups too), or are just offensive.
When people get called out for this behaviour, it can spark a big shitstorm of argument in which people often lose all concept of polite discussion and ask for rigorous proof that someone does in fact feel marginalised. This isn't very encouraging.
Links to geekfeminism seem to provoke a strong reaction from some people, but here's one for you:
http://geekfeminism.wikia.com/wiki/Male_Programmer_Privilege...
I encourage you to read this (even if you don't agree) and then spend some time on hn just thinking about the content of discussion knowing that some people might feel this way. Empathy is the key.
Not all of the examples on that page are applicable here because this isn't a physical space or a workplace. Yes, a lot of them are anecdotal - it's a wiki and a collection of peoples experiences. I'm not saying that you are necessarily privileged. Treat the page as it is - a collection of experiences.
I've bothered to type this out because you seem to be reasonable and to argue in good faith. To understand why people feel marginalised can take a bit more than logical argument though. You need to be open minded and to attempt to empathise with other people.