Placing turbines in underwing pylons began with early US jet bombers, the B47 and B52, and the C135 transport - later to morph into the 707. In his book 747, Joe Sutter (the lead engineer on the 747) gave the reasons for underwing pylons rather than the in-wing engine placement that was used on other early large jets like the Comet, Victor, and TU-16, as:
As to why over wing pylon placement isn't used... both reasons still apply.
Most maintenance on turbines is done on the aircraft - engine removal is not common, so the lower placement facilitates quicker average maintenance. Engine removal/replacement is facilitated with a forklift.
Catastrophic failure or fire... quite rare, but when it happens, the engine will normally drop off, away from the wing.
Also, under METO, the lower engine placement, under the CG, tends to pull the nose of the plane up rather than down, which is what one wants on takeoff or most situations where a pilot applies full power. Over wing placement would tend to pull the nose down on takeoff. A minor factor, but worth mentioning... no point in taxing the elevators more than necessary on takeoff, when control authority isn't the greatest due to minimal airspeed.
One rare exception to underwing pylon placement protecting the wing was AA Flight 191, the Chicago crash. Due to poor maintenance techniques, the rear engine mount on #1 broke, the engine pivoted upward, broke off, and went over and into the left wing, tearing out the hydraulics for the front spoilers. The pilots thought they were dealing with a simple engine failure, and followed the book for climb out with a single engine failure, maintaining an airspeed consistent with takeoff flaps set on both wings. Due to loss of lift from the damaged wing, the left wing stalled, and the aircraft rolled left into the ground. Not enough altitude to recover.
Having said that, this sort of catastrophic failure is quite rare, the most recent example being Qantas 32, an A380 that suffered a major inflight engine explosion. The engine did not drop off of the aircraft, and it was able to land safely, albeit with some degradation to control authority of the ailerons. Whether or not over wing placement would have resulted in more damage to the critical upper wing surfaces is a matter of conjecture.
One recent executive jet noted for over wing engine placement is the Hondajet. They include a short passage on the advantages:
A breakthrough in aeronautics, the Over-The-Wing Engine Mount was engineered and proven by Honda after more than 20 years of extensive research and development. This innovative technology not only breaks the conventional mold set by the aerospace industry, but also provides category-leading advancements such as a more spacious cabin, noise reduction, and increased fuel efficiency.