Weyl may not be really apologizing here.

It is more a confession and warning than an apology.

This could mean that it's very much an apology, but even more a confession and warning. Given the lack of any other apology-language, like "I'm sorry," I think it instead means that it's not to be read as an apology, even if there's a ruefulness about it. Even if it's an apology, he doesn't explicitly say that it's an apology to us. It could just as much be an apology to his supporters for misdirecting their attention.

He's speaking to his own community, RadicalxChange, at least as much as he's speaking to us. What is he saying?

Weyl thinks Silicon Valley is a villain.

... the technology industry, and especially Silicon Valley (SV), has become the greatest unaccountable concentration of power in the world today and is thus a fundamental threat to self-government. 

He thought that rationalists were soldiers in the SV army, because this sector is overrepresented in rationalism. Now, he realizes that he was mistaken. He dislikes our perspective, thinks we're wrong and self-contradictory, and that we're narrow in our demographics and influences. But he now realizes that we don't whisper in the ear of Elon Musk. He no longer sees us as any more threatening than the many other groups he dislikes, but doesn't bother to attack, such as religious fundamentalists.

Battling SV must be hard. After all, he has to figure out the anatomy of this large, complicated culture, and figure out which bits play an executive role and which bits are mainly just being told what to do. There's not much in the way of hard evidence for him to make that distinction. He had to rely on pattern-matching and associations to identify his targets. He thought we were part of SV's executive function, and now realizes that we're not. Given the enormity of the threat he perceives, he seems to have felt it was best to shoot first and ask questions later.

What's not clear to me is whether he'd resume attacking us if he changed his mind again and believed that we did have more power in SV.

On the one hand, he says "exaggerations of the group’s power and conspiratorial allusions are basically hateful and fundamentally opposed to my belief system." That sounds like "I was wrong to demonize rationalism because demonization is wrong" and a renunciation of the "shoot first, ask questions later" approach.

On the other hand, he says "However, what has changed significantly is my views of the sociological role of the rationalist community within the technology industry." That sounds like "I was wrong to demonize rationalism because rationalism isn't a high-priority demon," and a call to his community to train their firepower on a different target. Given that he's explicitly downplaying or denying an apology, I read this as the main point of his post. He's admitting an embarrassing strategic error to his own soldiers, not apologizing to us for the collateral damage.