I think the intuition is that it is supposed to be like a key. People generally do a pretty good job securing their keys. In addition, it is easy to have a backup key stored somewhere safe.
One nice thing about Yubikey instead of phone, is that since it only does one thing, you are far less likely to need to upgrade it. In the past, I have lost a 2 factor on my phone when upgrading since it is not backed up.
It’s like a physical key, also inside a combination lockbox, hanging from your keychain. It follows the Unix Philosophy in this regard of doing one thing very well and I think that’s a large part of the appeal.
Granted it does many things well, I think the most common case with Yubikeys is we only use them for one or two of their possible functions, and they’re cheap enough that this is okay; like a screw driver with half a dozen bits in the handle, but I just use the Philihp’s Head bit. In earlier Yubikeys, they could get stuck in PIV mode (like getting a bit stuck in your screwdriver), but I doubt anyone ever noticed.
That makes sense, and initially that is how I treated it, but essentially everyone I work with keeps theirs plugged in to their laptops 24/7. In fact, the keys we get as backups/replacements are the low profile ones designed to be plugged in and not removed without significant difficulty.
The effect this has is to make the laptop a "Something you have" factor. This works fine so long as the business is strict about ensuring people treat laptops appropriately and report losses quickly.
e.g. my last big corporate employer would sometimes randomly take any laptops that had not been properly physically secured during a meeting or over lunch. You'd come back and somebody groans "Oh no, we were only gone a few minutes". Yes we were, and you didn't bother locking your laptop so now you're going to have to grovel to somebody to get it back.
That’s why I love my 17 inch Alienware gaming laptop. If it is missing, I can usually spot the thief straining under the load of trying to carry it, and it is too bulky to fit in a normal backpack.
The only way to lock laptops to things I have seen have been Kensington slots, and those are literally security theater. You can cut them straight through their cables with a simple plier and zero effort, in one motion.
One nice thing about Yubikey instead of phone, is that since it only does one thing, you are far less likely to need to upgrade it. In the past, I have lost a 2 factor on my phone when upgrading since it is not backed up.