I think it depends on how it is said. "How are you?" is an an icebreaker, I think the intent behind it is more important that the actual meaning. When someone says "how are you" they arent really asking how you are... what they are really saying is "I acknowledge you, I am friendly, and I am open to talking with you" especially if its done with a smile.
It does annoy me a bit though when pleasantries are exchanged and the tone of voice is in complete contrast. If someone said "How are you" and were OBVIOUSLY displeased, or bored to see me then I would just feel insulted.
Small talk does grate me a bit, but I think its necessary... its the grease that allows more interesting conversation to come about. When you meet someone for the first time, you dont know anything about each other, so you have to convey your intent and your personality with generic meaningless chatter.