secure private key storage

in recent light of badusb

storing private keys on a usb flash drive is not the best way

what about writing private keys to a cd?

what i am worried about is whenever i plug my private key storage device into the machine, it opens up the possibility that any rouge process may take over and steal the keys

i have a private key used to encrypt all my other passwords and keys. this way i have a single key to worry about protecting. but it also opens up a single point of failure

how can i securely store this key?

i was thinking that a qr code printed on paper may be a great way to password protect a private key

but then that leads to how to securely decode the qr code and decrypt the private key