It's very simple really. The founders had firm Christian beliefs and because of that, they've been very open about their beliefs. It's no secret that Biblically based, Christian beliefs don't align with everyone's lifestyle. It was a business risk they felt was necessary for them to stay true to the vision of the founders. It's what they believe and they're not ashamed of it. That being said, you will never hear of them refusing service to gay people. They also hire openly gay people (Edward is a good example).
People who have a problem with this have a very simple solution. If you disagree so strongly with the stance Chick-fil-a has taken with sexuality, you can choose to no longer patronize Chik-fil-a. If you claim to have problems with their beliefs, but can't keep your fat ass from ordering their food, then you're just a spineless person with no will power who likes to likes to support certain "causes" so you can feel good about yourself.