Down votes are for communicating "I don't like this post." Flagging is for violation of community guidelines, or just plain abusive comments.
To respond to your claim, I'd like to point to you her blog post on the subject. She does a good job of explaining how she went from zero to being knowledgeable about physics in this post: https://fledglingphysicist.com/2013/12/12/if-susan-can-learn.... Essentially she always was interested in the subject but didn't believe she was smart enough to pursue it, until she was encouraged to take an introductory course.
That being said, in this particular case I have to wonder, what the fuck is the relevance of her physics credentials in this story? For one, she worked as a SRE and got hired based on her capability to do the job (whether you think interviews are a good gauge of job performance or not should be irrelevant), but more importantly does her being a good performer or not have __anything__ to do with how much she should be valued as a human being? Is blatant sexism and trampling someone's fundamental rights OK if said someone is low on the social hierarchy or meritocracy? The mere way this argument seems to be formed is fundamentally strange to me.
(I'm not sure about the threshold and I'm not sure if that is still enabled, because there are a lot of tweaks in HN that are enabled or changed without announcement.)
But sadly enough, people do use down votes for posts that they don't like, and flagging for posts that they really don't like. So it goes.
It seems the HN cultural practice is to down vote posts people don't like or just disagree with. I would rather people reply, but I can't do anything except for practice what I believe is right: I'll down vote a post that doesn't contribute to the discussion, as you do.
Since "doesn't contribute to the discussion" is vague and subjective, I can't claim particularly high moral ground.