Because it's an action against an entire company over one person's comment. The comment was not hurtful, demeaning, or insulting. The president never said "Gay marriage is wrong and Chick-Fil-A as company is against it". If the LGBT community was tolerant then there should be no issue here. There is an issue because people wanted drama and that's what they got.
that is a very myopic view you have. Saying that marriage should be between a man and a woman is the same as saying that two women or two men shouldn't be allowed to marry. Like it or not, he is the president of a company and by extension the face of the company. It may be his personal view, but he said it and others have the choice to disagree just like they can choose to either eat or not eat at CFA.
Both sides are trying to claim tolerance while being intolerant. Both sides are dumb.