i think its mainly because people with bone stock jeeps usually are the ones that just see them as a workhorse and nothing else. i think all people with modified jeeps understand and will give the wave back.
although im not usually one to give the wave, i just honk twice any time i see a jeep. if the person in the jeep understands, they will honk back. honking seems to be better than waving. but if somebody in a jeep waves at me, ill wave back because it means we both understand.
1996 XJ on 36" TSLs, 4", locked F/R, stretched