Some users are skittish of Chrome's autocomplete since it could potentially send anything you type into the address bar to Google's servers. Mozilla also makes money from selling 'search box real estate' to different providers. So it's more discoverable when the search is in its own designated box.
It's also what some of us frickin' want. I like having a separate search bar, because I can easily control which engine I'm using, and I from the URLbar I can search my history/bookmarks without irrelevant auto-complete results junking it up.
