I think this is a better example of the closed-mindedness and bigotry of the "Gay Rights" agenda than anything else. If a neo-Nazi walks into a Pizza Hut and orders a pizza, does that mean that Pizza Hut supports White Supremacism? Of course not, only an idiot would make that assumption. However, the Gay Rights movement loves to target Christian organizations, so it doesn't surprise me that they would go after a company like Chick-Fil-A.
The only intolerance on display here is from the Gay Rights activists.