I don't think I would boycott any business based on the owner's personal beliefs. I'm sure I frequent many places in which my ideology differs from theirs. Chick-fil-A made a mistake in advertising their beliefs (although they have a right to do it - however bigoted. Just as much as people have a right to boycott them). My politics are separate from my lunch. I don't really care.
As a business owner I think it would be incredibly stupid to entertain the possibility of alienating any customer base you have. Time will tell if it affects them long term. I don't think it will.