I agree, I find passwords on certificates useful in some circumstances and bothersome in others.
I think putting a password on a root CA certificate is just a bother without any REAL security advantages. First off you'll need to enter it on every restart, secondary the raw private key will need to be in memory after that (which is trivial to extract), and lastly if the machine is completely owned anyway, this seems like "rearrange the deck chairs on the Titanic."
Now putting a password on your SSH keys? Heck yeah. Otherwise if you forget to lock your machine just once, someone can sit down, open your SSH client of choice and have access to a remote session as "you" without the need for a single password. It might not be unbreakable but it is a nice extra layer of security that buys you time if your laptop gets stolen or similar.