Four words: Weight, Balance, Commonality and Maintenance. Oh, and aerodynamics.
The three engine design essentially means one engine at the nose or tail end of the fuselage. This causes stress on the fuselage (thus reducing lifespan) in a manner that it different to mounting the engines symmetrically on the wings.
You want all engines on the a/c to be the same, in order to minimise spares, crew training etc. When fuselage internal volume is at a premium, locating an engine in there as well is undesirable.
A fuselage-mounted engine is more difficult to access than one slung under the wing. This increases maintenance costs and turnaround times. This is a critical factor.
An engine (ideally) wants a "clean" airflow to suck in and push out. Therefore, (ideally), a fuselage-mounted engine would have air intakes at the front (or high) and exhaust at the rear, with the engine somewhere in between. This has structural, weight and accessibility implications.
Finally, why use three engines when you can use two? And if you need a larger MTOW, longer range etc., why use three engines when four will do the trick, at lower power per engine (thus increasing engine life), using variations on existing wing/fuselage designs (rather than new developments).
Not all of these arguments are applicable to all a/c and situations, but a combination of them means that the 2/4 engines, symmetrically mounted on the wings, is the preferred option.
The definition of a 'Pessimist': an Optimist with experience...