There's often a disconnect on HN between what HN users collectively know by virtue of this being their field of trade, and what the average non-tech person is aware of. It's this latter group of people that, by and large, as Bitcoin started to become popular, were under the impression that it was anonymous.
Edit: It doesn't help that, as the article states, Satoshi even said, "Participants can be anonymous," back in 2008[1]. To your point, he did say this as he linked to the white paper you mentioned, but average users are less likely to read the white paper than we are.
[1]https://www.metzdowd.com/pipermail/cryptography/2008-October...