Large commercial aircraft have low wings
- to easily stow away their long landing gears in the wing root,
- to hide the wing spar carry-through below the passenger deck,
- and to improve the accessibility of wing-mounted engines.
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 development cost of a single aircraft.
Pressurized fuselages need to have their passenger floor a bit below the center of the fuselage tube, leaving ample space below for cargo, systems and structure. Placing the wing high would produce a hump on the fuselage, which adds wave drag at the transsonic cruise speed of typical airliners.
The low position of the wing-mounted engines makes them much better accessible for maintenance; a major reason this configuration was selected in the early jet transports. Civilian freighters use mostly converted passenger planes, and their small number precludes custom designs. Initial concerns about foreign object damage (which resulted in a number of early jetliners with tail-mounted engines) proved to be unfounded.
Large high-wing airplanes 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. Also, the high wing reduces the risk of engine damage by foreign objects on improvised runways. That Lockheed likes to stretch their transports (C-130, C-141) anyway is the exception that proves the rule.
Turboprop-powered civilian airplanes may have a high wing in order to provide more space for the propellers. Here, the fuselage-mounted landing gear can be made short and light (which is how the Do-328 JET evolved). 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. Civilian transports will always either have a low or a high wing since nobody wants their passengers to climb across a wingspar carry-through on their way to their seat. At least since 1933.
* To be fair to the Avro engineers: The high wing position gives that airplane a very high maximum lift coefficient without requiring slats.