I don't mind when people do that at stop signs or where the bike path crosses the road. I give a wave or nod of thanks and a smile and carry on. Seems like they are just being nice. And it's not some sinister conspiracy against cyclists. I have a friend who does that to everybody at all stops. I think it's a way to take control of the situation rather than hope that others will obey the law.

I only don't like it when its done in such a way as to confuse everybody else. Or when people stop and wave me through when they don't have a stop sign. Probably because not only does it confuse everybody else but it confuses me, too, until I realize what's going on.