Because the designers KNOW that when they design the plane. So you configure the aircraft in such a matter as to (ideally) require no baggage management or other cg concerns to intrude upon operations. You're not going to get away with telling the operator "bad luck mate, this is an aft-engined aircraft, it's supposed to be a pest to load"! It's perfectly possible to have an aft-engined type with no more cg problems than a underwing type.
Where it becomes difficult, and what I was alluding to, is maintaining that design goal while also 'stretching' the plane to develop new models. Chances are that the original design concept, with a given fore/aft fuselage length ratio, will be harder to respect while stretching an aft-engined type, and THAT is I suspect what happened with the MD-80/90s. Especially as they changed the engines too, IIRC, which again is more of an issue since they have a longer moment arm than if underwing.
I suspect that the original DC-9s were not such a problem as the MD-80/90s, but that the loadability issue got gradually worse as it was sacrificed in favour of other concerns during development.