I think the issue is that I have a laptop at home and iMac at work so I don't bring my computer on my commute. Also, I like the extra security of the fingerprint scanner on my iPhone.
Your iPhone is completely covered with your fingerprints. Also, if your phone gets hacked/compromised the attacker could steal the secret used to generate your TOTPs. This is not possible with the Yubikey, it is absolutely impossible to extract the private key.
I have a Yubikey on my keychain (it can easily withstand this), and it takes very little effort to plug it into the USB port when I require it. Less than it would be to take my phone out.
As a side-note, some time ago the Yubikey had a vulnerability with its GPG module so they shipped out new ones for free. I now have the old key (with no GPG keys loaded on it) permanently plugged into my USB hub at my desktop. It is amazingly convenient.
It's probably a lot easier to steal your keys than it is to dust his phone for fingerprints and go through all the trouble of then faking the print on the sensor.
Heck, all someone needs to do is grab the one permanently plugged into your USB hub on your work desktop after you've left for the day.
It's my desktop in my home. If someone breaks in (or steals the other yubikey from my keychain, and thus has the keys to my home) I have bigger issues. And they still won't know my password.
In that case, I might prefer an authenticator to a keyfob that requires insertion too. The yubikey is slightly more secure since it's actually signing a message from the server rather than sending a password that can be (briefly) intercepted and replayed. But it's probably not 'better enough' to encourage someone not to use 2FA at all if U2F isn't convenient.
If user security has taught us anything in the last 20 years, it's that security features have to be convenient or may as well not exist. I think we'll be seeing a lot more 2FA options in the next few years. In this segment, user choice is a huge improvement in and of itself. I've also been testing Duo push for some internal stuff, which is a phone-based experience that's as smooth as silk. To each their own!
I have a Yubikey on my keychain (it can easily withstand this), and it takes very little effort to plug it into the USB port when I require it. Less than it would be to take my phone out.
As a side-note, some time ago the Yubikey had a vulnerability with its GPG module so they shipped out new ones for free. I now have the old key (with no GPG keys loaded on it) permanently plugged into my USB hub at my desktop. It is amazingly convenient.