How many atheists do you think there are across the country that would be willing to donate $20-$50 to air such an ad? If a 30-second ad is $2 million, it would take 100,000 donations at an average of $20 per person. For an average of $50 per person, we'd need 40,000 people to donate.
Perhaps some prominent atheists, like Dawkins, Dennett, etc., and maybe even those who aren't especially vocal about being atheists, like Bill Gates and Brad Pitt, would be willing to donate a few thousand to such a proposition.
Another issue is whether Rupert Murdoch and Fox would be willing to air such a commercial.