Of course, you peel a banana from the top. The stem is there to provide the perfect handle for peeling. You just grab, snap, and peel–easy enough.
Be honest with yourself: the function of the stem is to act as your gateway to the banana fruit itself. Can you imagine that stem hanging down from your upside-down banana, unused? No.
Peeling a banana from the bottom is the more efficient route. You simply pinch the bottom and peel. There's no concern about wiggling the stem back and forth to get it to snap–you get it right every single time, and your banana will never suffer in the process.
If this feels like sacrilege to you, take solace in the fact that this is the way nature intended; monkeys peel bananas from the bottom. And wouldn't they know? Flip your banana upside down and enjoy your un-mushed fruit.