
I think that bigotry is what we are dealing with and that identifying it as such may help. I also suspect that "bias" is sufficiently vague that many theists won't get the message. Some won't recognize their own bias and won't be sure what "bias against atheists" would look like. Others will embrace being biased because...well...atheists are evil and so bias against us is justified.
In contrast, "bigotry" has a much stronger emotional impact. People are much more likely to recognize it, and such a message would do more to prompt some self-reflection. At least, it should.
I still like the ads as they are, but I think they'd be more effective with this small change. After all, we're all biased in some way or another; bigotry is another matter.