I say "simply" because, as I mentioned, it's an invariant—possibly the most consistent phenomenon we've observed on HN [1].
But if it's so consistent, how can it go unnoticed for long (as you've reported) and/or get perceived as one-sided ("HN is so anti-A") when in fact it is usually two-sided ("HN users are divided on A")? The answer is that what you notice depends on how you feel [2]. If you like A, or (more precisely) if you dislike anti-A, you are far more likely to notice anti-A posts. Not only that, but you will weight them more heavily, meaning they make a stronger impression on you than the median post does—even the median pro-A post.
These two variables, frequency and impact, combine to produce a picture of the site as anti-A—so strongly that people often use universals like "always" and "never" when describing it. In reality, HN is a statistical cloud, but your pre-existing feelings determine which datapoints you happen to notice (frequency) and how strongly they affect you (impact). [3]
This is why people with opposing views feel the same about how biased HN is, but in opposite directions: A is certain that the site is anti-A, and B is just as certain that it's anti-B. Their feelings cause them to notice different datapoints. Abstract out the directional bit (pro- or anti-, A or B), and their perceptions become isomorphic.
Unfortunately for us, HN is more afflicted by this than other sites of comparable or larger size, because all of them organize the community into silos [4], meaning they're sharded by social group (like Twitter's follow lists), or by content (like Reddit's subreddits), and so on. HN is non-siloed, meaning everyone is in the same place: all the As, all the anti-As, all the Bs, all the anti-Bs - we're all roaming the same threads and bumping into each other. You are therefore more likely to run into datapoints you find disagreeable, and thus to feel that the community is biased against your view, and - what's worse - more biased the more strongly you feel!
Once or twice a year, some reply I'm writing gets hijacked by my sadness about this and turns into a digressive lament. Why sadness? because although I believe that in reality HN is somewhat (<-- not to exaggerate) more thoughtful and tolerant than other communities of the same or greater size, this dynamic means it inevitably gets perceived as less so. [5]
I believe this is why one so often hears about how toxic, nasty, negative HN is—not that it isn't those things! but the relative level of them gets distorted. Humans can't take much of what we dislike and disagree with before resorting to generalization and other internal barriers. This is essentially an immune response. It often takes only a handful of datapoints (3, or 2, or maybe even just 1) before the impression burns into the retina and becomes permanent [6].
This is most painful when the topic is close to one's heart—for example, when one's own work is being criticized. In cases like that, it doesn't take much before one feels wounded, and such impressions rarely go away.
In one case I saw, some people were agreeing about how terrible and mean Hacker News is, and to prove the point, one of them linked to a vile reply he had received. That reply, however, was from Twitter—not from HN at all! He hastened to add "HN is the same"—somewhat self-refutingly, since if it were true, an actual example would not have been hard to find. In reality, while such vile comments do show up on HN, the community quickly flags most of them, and moderators eventually flag most of the rest.
That is an example of the skew in perception I'm talking about, and even though it made me feel terrible, I can't be too critical because I understand where it comes from. It comes from fundamentals [7]: specifically, how HN's design interacts with human hard-wiring. Because those are fundamentals, this is not going to change, nor can it be affected by argument. Sad!
Or rather, it could only change if we changed the foundation of HN's design—in this case, by sharding the site into silos—but (a) I'd be scared to tamper with DNA at that level, and (b) if the above is correct, then it's good for the world that this place exists. It just can't expect to be perceived as such [5]. End of this season's lament.
[1] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
[2] I don't mean "you" personally, of course—everyone does this. It's a double whammy of https://en.wikipedia.org/wiki/Negativity_bias and https://en.wikipedia.org/wiki/Clustering_illusion, sometimes described in this way: https://en.wikipedia.org/wiki/Hostile_media_effect.
[3] Lots of past explanation here if anyone wants it: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que....
[4] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
[5] I wrote a thing about this a few years ago, if anyone is interested: https://news.ycombinator.com/item?id=23308098
[6] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
[7] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...