I'd say the main reason is aerodynamics, i.e. efficiency. There has been generations of engineers calculating it through. I read an article once (sorry, couldn't find the source) that you need less structural strength compared to the size of engine/aircraft with underwing engines, since the propulsion source is right on the center of gravity, the center of lift and (most of) all axis.
Before noise reduction I would also mention the safety factor of having engines as far away from all vital systems and passengers as possible. We all know of some uncontained engine failures that led to complete system failures with fuselage mounted engines while so far its rare to do the same on an underwing design (that's why the engines are mounted in front of the leading edge).
Anyone agree?
Dani