pretty often they're just being jerks who think their pride would be hurt, but there are a couple of other reasons you may consider...
sometimes of course they may not see you wave, or it may be too late when they realize, but there is one major difference between the two that may also be a factor...
On a scooter, especially a 50cc automatic, your left hand doesn't really do much but occasionally brake and maybe change headlight intensity or blinkers, but a motorcyclist uses both hands actively to drive at all times. their clutch is on that side... so whereas most of them are too cool to bother, looking like jackasses in the process, but every now and then its just not possible to use that hand to wave because its covering your clutch or shifting or something of that sort...
usually when they don't wave I just think well hey, they just looked like a jerk and I just looked like a cool friendly guy... if they think its below them to wave then they can prove how much of a pompous twit they are by not doing so...
I believe in the wave... I think ALL riders on two wheels face much the same challenges on the road.... BOTH contend with weather and other drivers, both have trouble with slick roads and people turning, or pulling out in front of them unawares, and bottom line is, BOTH of them could end up smashed up on the side of the road one day and it could be that same scooterist who you were too stuck up to wave to that could pull over and save your life...
That's something I try to remember... another bike rider is the most likely to help you out if you find yourself in a bad spot, and they are the most likely to recognize your distress...
we all should respect each other on the road
and even if you're too busy to wave, you're never too busy to give a friendly nod...
just forgive me if I don't see you in time!