The current release does not allow to specify a passphrase to protect the private key related to the personal certificate. I will try to solve this problem in the next release.
At the moment you can just use openssl suite commands to encrypt the private key associated to a X.509 certificate.
Let me know if iPhone uses base64 (.pem) or pkcs12 certificate format and so I will post the command to do it.
Regards
Fulvio