I mean . . . I don't wave to every Dodge Ram 1500 I pass, why every motorcycle?
I think it has more to do with cult vehicle status. In the cage world, it is ususally more specific to a model, but biikes just seem to get lumped together more... except some cliques are less likely to wave at riders of something outside their clique. I think as more and more motorcycles appear on the road, it will probably break down into cliques even more - or just go away. I still wave, but not usually in the urban areas unless I'm waved at first. I've got better things to spend my attention on than look out for other bikes to wave at.
When I was growing up, 4x4 drivers would always wave at each other, now it tends to be more brand/model specific. Jeeps wave at each other, but not to Toyota drivers and vice-versa.