Corey lives in San Antonio. We met years ago when we lived in the San Francisco Bay Area. Both of us ride bicycles and motorcycles. Here's what he had to say about waving among both subcultures:
I notice that when I'm on my bicycle and wave at motorcycles (which I do routinely), I get more waves back than when I'm on my motorcycle and wave to bicycles (which I also do routinely).
I think it's because there is a stronger fraternity of motorcyclists than bicyclists. Riding motorcycles is a lifestyle whereas riding bicycles, for most people, is a pastime/hobby. Most bicyclists don't get "Colnago" tattoos and go to big rallies. Occasional centuries, yes; rallies, no.
There is more of an "us vs. them" mentality amongst motorcyclists. Most bicyclists (unless they also ride motorcycles) don't know the term "cager" and, for them, the fact that they are on two wheels does not mean that much (since they probably parked their SUV at the ride start and they will soon be back in their own cage).
Before cycling got popular, there was more waving going on. I think, back in the day, folks would get into cycling through clubs and cycling friends who would show them the ropes (and teach them about waving). Now, folks read about bikes in magazines, go buy a new bike and start riding on their own, not knowing that they're picking up bad habits.
I'm not sure that there's much that can be done about it. The nature of the sport may have changed, for better or worse, irreversibly. Maybe some of those who choose cycling will stick with it and join a club and become part of the tradition. Let's hope so.