This happens to me on an almost daily basis and for some reason it really annoys me. I've even had people stop in the middle of the intersection as I approach and try to wave me through in front of them!
Now I realize that this is mostly due to San Francisco "cyclists" rarely stopping at stop signs, so drivers have been conditioned to just let them through whenever they approach a stop sign. But I have had to literally stop, put both feet down, and pretty much yell at people to get them to just go through the intersection. Then they look at me like I'm crazy. Damned if you do, damned if you don't I guess...