I've never ridden a motorcycle but I always thought they waived at each other because of the increased risk of riding bike, sort of as a respect/acknowledgment/ type of thing, just making sure they were all ok and what not.

I figured why not do the same to bicyclists, just saying hello, I always find I feel better when people wave back in a joyful way. I agree that roadies tend to not do it so much, but whatever.

Besides its a good way of keeping my attention on both directions of traffic, in fact if I didn't wave at people I would have completely passed a friend last week without noticing it was him. So I just figure whatever, wave if you want to, if not don't.