The vulnerability, as another commenter mentions, is extremely hard to exploit and requires both physical access and the specific accounts to clone the key for.
That may be too much of a risk for enterprises, but as a personal security key? That seems like a completely reasonable choice to make.
But a software password manager on a compromised computer can be compromised, right? It feels like the secrets can't be extracted by a compromised computer: the attacker needs physical access to the Yubikey.
This sounds better than a software password manager, right? Or am I missing something?
No, I'm not. I've got a bunch of yubikeys locked in lockboxes when they're not in use, serving as trust anchors for internal PKI, but also using certificate logging. If one is compromised, there's a short window until it's known, and access to the box has a very small group of people. My threat model does not include "Insider under the watchful eye of two other insiders"
The attack is local, limited, and requires sophistication to pull off. For most people and most use-cases, this is a theoretical vulnerability rather than a real one.
While some users may need to buy updated YKs, perhaps having a tier of discounted "vulnerable" new old stock and more expensive patched new stock would make the most economic and utility sense.