Bike messengers aren't commuters and have specific needs that other riders don't have. Bike messengers make a lot of very short trips and are constantly getting on and off of their bikes. They may get on and off three times in one block if that have that many deliveries. Because they are always hopping on and off of the bike, it's much more efficient to have something on their back so they don't have to stop and fiddle with panniers. The single strap makes it quick to take off, and the shape is designed to carry large documents without having to fold them. The fact that they can be kind of unstable doesn't matter for the short distance between deliveries.

Commuters, on the other hand, get on the bike at home and off the bike at work, or vice versa. The disadvantage of being able to not instantly hop off your bike is pretty minor when you are only doing it at the end of your trip (and most messengers here just use one small U lock to lock up, relying, I think, on the fact that they won't be inside long, while commuters tend to lock differently if their bike will be outside all day).

For commuters, the disadvantage of having something on your back is compounded because of the distance spent commuting and - depending - on what you have to carry.