On my recent trip from NY to L.A. and back I had an iPad in a small shoulder bag packed inside a carry-on with wheels and a handle. They had me take the iPad out of the carry-on but I could keep it inside it's own shoulder bag. They said that as long as it was separated from the rest of the luggage it would be fine. I did not have to take it out of it's bag.
On the way back they took the iPad bag out of the grey tray where the shoes and belt and jacket, etc. were, and told me they were running it separately through the machine. It was fine then.
Funny too, I could see and hear the guys checking the screens. One guy smiled and pointed to the screen, "there's an iPad!"