Make sure you are using the latest version of Unity and the latest version of XCode.
Then try the Image Targets sample and check that auto rotation works (and it does).
Then compare this with your own sample and code in order to identify the difference.
This should help you work out what the problem is.
I have a unity app with iOS native part, the rotation work ok in iOS's part, but wrong in unity's part...
However if you mix native iOS and Unity then this may be causing you further problems if the orientations become out of sync.
In order to try and solve this you need to tell Vuforia to rotate when your native iOS rotates, and the API to use here is:
You can find examples of this by searching through the XCode project in iPhone_View.mm and UnityAppController.mm