You have to realize Jeeps are no longer just made/used by offroaders who really get into the whole Jeep thing. Since the introduction of 4 door models with fancy interiors, those models are predominantly being bought by people who have zero interest in their offroad abilities.
If I'm going to expend the energy to wave, it's going to be directed solely at a Jeep that is obviously into the Jeep-thing. Clues like having a winch, big tires, battle damage, etc. will get my attention. A pristine Jeep, especially withy 4 doors, with Armoralled tires on 18-20" wheels won't.
And the wave thing isn't just about Jeeps. Also included are owners of sports cars, Porsches, Harley Davidsons, or other unique vehicles with a following.