The issue isn't so much his stance on equal marriage (although that is part of it), it is the fact that he uses profits from Chick-Fil-A to fund hate groups, such as the family research council, that are trying to strip gay people of their basic human rights.
Also, he DID say that equal marriage is wrong - "I think we are inviting God's judgment on our nation when we shake our fist at Him and say, 'We know better than you as to what constitutes a marriage'. I pray God's mercy on our generation that has such a prideful, arrogant attitude to think that we have the audacity to define what marriage is about"
This blog post covers it better than I have here -
http://www.owldolatrous.com/?p=288