The Chick-Fil-A analogy does not work because the cake was being asked for a special occasion which the bakers could not support because of their religious beliefs. Of course I can't be sure, but my guess is that the bakery would have been happy to serve these folks if they came in and just wanted to buy a few cookies.
Here's another way to understand it. I'm a professional singer. If a gay couple were to approach me and ask me to sing at their "wedding," I would refuse, citing my religious beliefs. However, if they came to me and asked me to sing at their cocktail party, I would agree -- just another gig. Because a wedding/marriage ceremony to me is sacred, I have the right to refuse based on my sacred beliefs.
Also, discrimination is not applicable here because homosexuality is a choice, where race and gender is not a choice.