The reason depends on your "mission" . Underwing engines let you have bigger more efficient engines. This also make maintenance easier. The down side is you need long landing gear and they could suck stuff in when on the ground. This puts the aircraft body higher off the ground so you need extra stuff to get people and cargo in and out. So if you need your aircraft to be low to the ground or take off from dirt or grass you have to mount your engines up high. This why lot smaller jets have the engines mounted up on the tail. Down side is this also limits how big they can be, but now your aircraft can sit lower to the ground and not need things like a jet-bridge or extra equipment to load cargo.

Something to note is when you look at aircraft like the older 737 and A320. Boeing wanted to make the 737 as low to the ground as they could wile keeping under wing engines. This is why they have that odd pouch shape. Airbus just keep the landing gear longer. 737 was designed with the idea that could go in airports that might not have the gear to load cargo in to a taller aircraft. Also the newer regional jet tend to have engines back on the tail. same thing they need to be go in to airports with out jet-bridges.