While the comments of Chick-fil-a president and chief operating officer Dan T, Cathy about gay marriage were ill advised, he does have the right to say it and people boycotting the store have all the rights in the world to hate it. It should be no surprise he made such comment as the store is open in its traditional stance on the family. his comments are anti gay marriage but this no controversy as the company was founded by a baptist preacher so expect a ham-fisted comment about gay rights or two.
This is great example of fake controversy as he didn't say he 'those gays should be damned to hell cos my god says so' or 'if i had my way, ill shoot those sissies and let god sort 'em out' or put 'no queers here' signs outside chick-fil-a stores across the nation. While it does set a serious precedent that a head of a corporation takes a strident stance on a issue that literally split the country down the middle, he does have the right to take such a stance nonetheless.
Regular customers also have the right to boycott or take their business elsewhere if they don't like the stance of the corporation on any issue they hold to be right or true as it is their right to choose where they spent their money elsewhere and/or boycott the store. The controversy is not really over free speech as there is no question he has the right to say what he did, but what he doesn't have a right to is to tell anybody who disagrees with him how they should feel or react to his comments.
Only in America can such a issue cause such a furor as other nations do not make national and global news due the stance of a company on a issue that barely penetrates the nation conscious and almost nobody (unless they are part of congregation) bats an eyelid.
In sum, while he shouldn't have said it he right the right to say it nonetheless and boycotters also have the right take their business elsewhere or to take protest outside branches of Chick-fil-a. this controversy is not a debate about free speech or even about gay marriage but of choice and sooner all parties involved realize that they all have the right to choice, the quicker the debate dies down.