Actually just a few months ago polls in the US for the first time started showing a majority of Americans now support gay marriage. That doesn't make the statement you were quoting right however as even if a town wants something, they're not allowed to violate laws and the Constitution to have it.
I agree that even if I find the Chic-fil-A executives words to be despicable, he has a right to say it. And people who think that he's a piece of crap have the right to say that and to boycott his business. If he'd come out and said he thinks interracial marriage goes against God's will and that makes us as a nation arrogant, quite a few more people would have had a problem with what he said. But in the end it's the same thing substituting race for sexual orientation.
The mayors of Boston and other cities also while being elected officials, still have the right to free speech. They have the right to say "Boston doesn't want you in this town". However if they try to use their position as an elected official to punish Chic-fil-A for the speech of their executive, then they are violating the First Amendment. Right now what these mayors have said is rhetoric, we've yet to see if they will attempt to act upon it.