I agree that it's difficult to see a person in a car waving you on. That happens fairly often around here- a car will wave you by/through even if you don't have the right of way. Since I pretend to be a car on my bike- that's confusing to me. Sometimes I wave them through and they wave me and we both go at the same time. huh? ooops?
I think it's just people being kind, but it's still confusing nonetheless. I almost always assume the car will not stop nor see me and am always in preemptive strike mode- ready to be clobbered at any time.