If you are short-hopping, and auto-cancelling the Bair, that means you stated the move as soon as you could. So if it goes over your opponent, that means you're fighting a small character, and you simply can't hit him that way (although badly spaced bair hits a little lower than good spaced bair). From there, a few solutions:
-don't do the bair as soon as you jump, but a little later. You'll suffer the landing lag, but if you space it correctly, it can be safe on some characters' shields.
-don't do autocancelled bair vs small characters. Don't try to hit small characters at neutral with bair at all. Unless you are reading an option or something. Short hop autocancelled bair goes over small characters, and leaves you open. Especially when used oos and close to the opponent. It just begs to be dash grabbed.
-space your rar aerial well enough so that even if you whiff, the opponent can't punish you. Think of that bair as a way to counter a possible aerial option from the opponent, but don't absolutely try to hit him. Best case, you hit him if he jumps, worst case he doesn't jump, doesn't get hit, tries to punish you (dash grab or w/v) and you punish him instead because you baited him with your awesomely spaced bair.