I'm still unsettled on this, but I think the answer might simply be to keep atheists coming out of the closet.
I was eating lunch with a friend of mine the other day. He's semi-religious, but not in a church-every-Sunday kind of way. He's smart. He loves talking about science. Doesn't have a problem with evolution. And yet even he was shocked when I used the A-word to describe myself.
Clearly, not enough people have met enough atheists to realize that we're actually normal, decent people. While I'm not sure that I'm completely on board with hanging a scarlet A outside my door (per the Richard Dawkins "Out" campaign), I do think that it would cause a major shift if people actually realized how many of their friends and neighbors are atheists.
I guess not being afraid to identify yourself as an atheist is a good start, when the topic comes up, and in a non-pushy way.
Hey, what about an international atheist day, in which all atheists would do something small but identifiable, like the ribbon campaigns for cancer awareness, etc. It might be surprising to see how many ribbons suddenly appear on that day....