People will only use your product if they know about it and perceive value in it. How do people know about it, and why would they want to use it?
On "Most of the tiny number of real users have come from links posted to places like Hacker News, and there is almost no organic traffic from other search engines" - Organic traffic comes from word of mouth. Are people talking about your site? If they're not, you're not gonna see organic traffic. You could do what others do and pay some influencers to advertise your site, but that's expensive and not as scalable as "real" buzz. Is your product exciting or controversial? If not, why would people talk about it?
Your homepage's tag line is "Open source search engine and search as a service for personal and independent websites." A regular person's eyes would glaze as they try to figure out what this means. Given some time they might put together the words "search engine" and "personal" and "websites" and figure this is a blog search engine. So just say that.
The "Newest Pages" section is a fun novelty, but after a few minutes the novelty wears off.
The "Browse Sites" section is almost useful. Next to the list of sites I see some tags. Why isn't a heatmap of the tags the first thing I see? That would be way more useful than a paginated list of random sites.
Your "About" page lists "community-based approach to content curation". This is the most exciting aspect of the whole endeavor, so add that to your front page blurb ("Community search engine"). You would probably do well to build a real community around it, for example with a forum or chat system (GitHub Discussions does not count). A SubReddit would be an easy way to bootstrap this and later move it to your own hosted forum.
You'll probably need a very complicated moderation system if this thing takes off.