Most jet engine intakes are round which allow for a smooth airflow into the compressor of the engine. Generally it is beneficial to mount the engines to the wings, and if the wings are not high enough off the ground, two problems develop.
First, the jet acts like a large vacuum where extreme low pressure develops ahead of the fan intake and sucks in anything in its path. If the engine is too close to the ground, the risk of ingesting rocks, standing water or snow, and other foreign object debris increases. Ingestion of any FOD can be catastrophic to the engine causing it to fail at one of the most dangerous times in a flight: takeoff.
Secondly, more ground clearance is warranted because of crosswind landings. When a crosswind landing is being performed, one wing will be lowered to maintain the airplane on the center of the runway. A lower engine might strike the runway surface during this maneuver.
Engines that have an oblong shape like the pictured Boeing 737 try to increase ground clearance by rounding off the bottom of the engine tighter than a perfect circle. A negligible amount of engine performance is lost by doing this.