Correlation -> Causation?
Is that seriously why you think there aren't more women on HN? Because it's offensive and exclusionary against women?
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.
This seems to be something of a hot button issue within the community at the moment, probably spurred on by pg's comments taken out of context, but the last few threads on similar topics have been filled with bile, reverse sexism claims, and general attacks against women. It's sad to see, because at this stage it's essentially too late for this place. The last community community I was (and still am) a part of made a conscious effort to change its moderation and terms of use to be more inclusive and punish individuals who stepped over the lines, but it was too late for them too - the sense of community was already destroyed for most of the visibly female members there. I haven't noticed them come back.
I live in Arizona. When someone cuts me off on the freeway, my instinctive response is to look at the license plate. If the license plate is from a northern state, my reaction is "Fucking snowbirds. Goddamn." I'm in my car, and I'm just reacting - I'm not thinking. Five seconds of thought calms me down, but until that happens, I'm making a pretty nasty comment about the elderly.
The Internet is similar to my car - it's a consequence-free space where people can just say things without thinking. The difference is that unlike my car, where I could spout off the worst racial profanities I can come up with, the Internet actually has people reading the posts.
As for Internet communities being devoid of women, I can think of exactly one general community that has women. It has three things that I think are vital - a small community, a draconian moderation team, and a userbase that calls out bullshit very quickly.
I haven't read the entire thing, however.
Would you mind sharing a link?