High winged aircraft, as they are called, can avoid FOD damage easier. This is important for military jets but not for airliners.
High wing gives:
- Harder engine maintenance.
- Wing box goes through the cabin instead of the lower fuse.
- Better engine ground clearance.
- Tricky undercarriage construction. Either in the fuse or on long legs on the wing. Neither method is optimal unless you want the fuse sitting very close to the ground. This is ok if you have a sloping rear fuse due to a cargo door, but that kind of rear fuse makes it hard to install seats all the way back.
- Closer to the ground is good if you are loading outsize cargo. For pax and normal cargo it's less of an issue.
- I will leave the aerodynamics to the experts
One of the 747 concepts was mid winged and double decked btw.
"There are no stupid questions, but there are a lot of inquisitive idiots." - John Ringo