The wing-fuselage intersection is a significant cause of drag, and this is supposedly much worse on a high wing than a low wing. It is also very inconvenient for undercarriage mounting arrangements. Look at the RJ100 for example. The whole arrangement of sponsons to house the main gear and heavy frames to transmit loads from the undercarriage to the wing root are very awkward, and add a lot of weight to the airframe. Low wing configuration is structurally simple and also a good comprpomise aerodynamically.