I have to admit, I don't wave at stock Jeeps very often either, and only people I know wave to me. There are a ton of JKs up here, but I'd attribute their choice of vehicle mostly to how bad the roads are up here. I'd say 95% are stock and never go off road, and that their drivers don't have the Jeep mindset.
When I bought my Jeep in Ontario it was different. Most people waved / waved back. But that was also when I lived in a city where anything can drive around easily, so it's more likely that they bought the Jeep to be a Jeep and not just any old SUV. I'm pretty sure most of the Jeep owners there understood the Jeep wave even if they don't actually go off road with them.
That said, even though my Jeep was stock (and for the moment still is), it's a special edition that came with an upgraded hood, bumpers, etc, so that might make a difference for who waved at me too.