The TSA ruled on Tuesday that iPads may remain in their bags for scanning. Since they're relatively small with no bulky AC unit (no word if this needs to be scanned separately), cables, external drives, etc., they're just as easy to examine while inside your bag.
You could be asked to remove it if the agents can't get a clear picture, so don't bury it under a heap of socks and underwear. Conversely, laptops must always be removed from their bags and scanned separately (at least that's the rule at BOS).
As for your shoes and belts, well...expect to drop them into the tray, too.