My point has never been that businesses (large or small) shouldn't be able to discriminate. My point has always been that the law currently forbids discrimination by public accommodations, and that the nondiscrimination should be across the board, not just for everyone but gay people, or by everyone except those claiming a religious basis for their discrimination.
Churches are not public accommodations, they are houses of worship. Many functions of churches outside their actual worship services and buildings have also been protected under law and judicial precedent. This is a category of special protections that even some churches and fraternal organizations do not enjoy. But there are limits to this (and all) exceptions. A church or a fraternal organization cannot simply slap a cross on whatever they do and call it "religion". And neither can a business which advertises and is open to the public. Right now, that's the law in many places.