on his blog. The upshot is, the hacker used social engineering to get Apple to give him Honan's password. There really isn't anything you can do to stop that.
Honan's problem got worse because all of his accounts are interconnected - his Google, Apple, voicemail, Twitter, etc. all share credentials, allowing the hacker to use one account to compromise many. Honan offers a detailed description on what he would have done differently. This is a great reminder to do some house cleaning of our own accounts.