Why do most commercial aircraft have their fuselage over the wing, instead of under?
Large commercial aircraft have low wings to stow away their long landing gears. Long gears make it possible to stretch the fuselage and still be able to rotate during take-off. Stretching makes it possible to tailor one basic design to a wide range of sizes, lowering the price of a single aircraft.

Large high-wing aircraft with their low fuselage position are easier to load and unload, at the price that the fuselage taper has to start shortly aft of the landing gear, so no stretching is possible. The military doesn't mind and prefers the high-wing variety. That Lockheed likes to stretch their transports (C-130, C-141) anyway is the exception that proves the rule.

Only turboprop-powered civilian aircraft may have a high wing, so there is more space for the propellers and the landing gear can be made short and light. Still, both versions exist. And the ones where the engineers did not know how to attach a jet close to the wing.

Aerodynamically a mid-wing position would be best. This is used when the payload is compact and needs little space, or is hung externally. In bombers, in other words.

In terms of stability and control both configurations are equivalent.