Yep, I managed to get it working in the end, the step that is missing is that you need to manually copy the certificate and provisioning profile over to the the iPhone your testing on. Just hook the phone up to iTunes, let it sync etc as normal, and then just 'drag' the certificate & profile over to the phone, and it should sync them across. If they've synced across succesfully you should be able to see in the settings app that its running your development profile, and then the App should correctly sync.
I am doing this using Windows FB4.5, iTunes 10.5.3.3 and iOS 5.0.1 (iPhone 4s) and have followed the instructions as per http://www.adobe.com/devnet/air/articles/packaging-air-apps-ios.html
Wrt the post saying that it works if you copy the cert and provisioning files onto the iPhone there is no mention of this in the windows instructions. I did try to do this using windows explorer and got an error message however. Does anybody have any more information about this problem as I am unable to even get a Hello World installed on the iPhone.
If you go into the 'General' tab of the 'Settings' app on your test device, do you have an entry one up from the very bottom called 'Profile' and showing the name of the provisioning profile you created? If you can't see the Profile entry there, then you won't be able to Sync the test App.
I ended up giving up on iPhone Dev via FB, although it was a little more friendly than xcode, the basic control set was just far to limited for general purpose development.