The point is that ssh keys lying around on your laptop aren't the greatest idea either. Where is the root of trust? The password you type to terminal if you encrypt them?
FIDO2 starts with the idea of safe defaults, where either client devices (Android, laptop TPM,...) store the keys safely, or dongle vendors (like us, SoloKeys). These have a business interest in doing their job properly.
But there's nothing preventing software implementations, it's an open standard in that respect (I do have other issues with it but your specific concern is unfounded imho).
FIDO2 starts with the idea of safe defaults, where either client devices (Android, laptop TPM,...) store the keys safely, or dongle vendors (like us, SoloKeys). These have a business interest in doing their job properly.
But there's nothing preventing software implementations, it's an open standard in that respect (I do have other issues with it but your specific concern is unfounded imho).