He said that he took it down after he calmed down about 10 minutes later. Clearly enough time for someone to snap this photo and take note. He has since apologized and now the debate over whether to accept his apology is being fought.
http://redd.it/mkw6h
Now PZ Myers of Pharyngula fame has been vocal about not accepting his apology. The owner has made a personal apology to PZ which he rejected saying "I have to live with the fact that I live in a country where my rejection of your religion makes me a pariah. There’s absolutely nothing you can do to make up for that." I certainly understand where Pz is coming from and I would not patronize his store myself either. That being said, we all make mistakes and have knee-jerk reactions, and I believe that is what probably happened here. I don't know what he could do differently now that will make it up to anyone.
http://freethoughtblogs.com/pharyngula/2011/11/22/fair-weather-atheists-and-sunshine-skeptics/
Often there are times when public figures make some off color remark or mistake that they are forced to publicly apologize for. When I see these, they frustrate me, because I know that person is just doing it because they have to. They don't have a different worldview just because they apologized. A racist isn't not a racist just because they apologized that their statement was overheard. So I don't think that just because he apologizes that he will think any more of skeptics or atheists. Likely he is just sorry for his overreaction not his belief. He also claimed that while the sign was up that no one was refused service. In fact he may have done some people a favor, after all who wants to give their money to someone who is that bigoted. So, I don't know if he apologized just because he thought it would be good for business, but I can accept his apology, however if I find myself in Springfield I wont be giving him my money.