It is not as flexible.
I am at my friend's place and I get an alert on my phone that someone wired some money out of my bank account! I need to login to my bank's site to check whats up. But, my public key/cert is in my computer and I have not registered to the bank using my friend's machine. Or I forgot to carry my Yubikeys with me. Now what do I do to quickly login?
It does not have the necessary client support yet.
We use webauthn for some of our internal workflows in our organization. It works flawlessly for web browsers but it doesn't have the necessary support for other clients yet. For example, there are several applications that run as Desktop clients on Windows/Linux/Mac etc.
If you look at the support matrix on FIDO alliance's website, their support for some scenarios is still work in progress:
Electron is a popular application framework based on Chromium browser. It doesn't have a clear answer for U2F support yet. Some users claim it works while some can't get it to work.
If your application is going to be supported outside of just a browser, then currently you don't have much choice.
One of the major device makers, Apple, joined FIDO alliance to move users away from passwords as late as Feb 2020. So, there wasn't enough urgency to even support many of the user scenarios.
It is not an easy job to replace passwords entirely
Getting rid of passwords means changing user behavior. That takes a while. Here, usability of your security mechanism plays a huge role.
Before Face ID, Biometric auth in phones and Windows Hello, there was no cheap way for general public to use anything other than passwords to login. And these are fairly recent technologies.
Mobile phones have done a great job so far of integrating separate authenticators like Swipe patterns, biometric etc to replace passwords. But till we get such easy and free technologies available to mass market for Desktop, it is going to be hard to replace the passwords.