The whole boycott culture is pretty silly. Conservatives threaten (who knows if these things have any substantial effect) to boycott J.C. Penny for hiring spokes person Ellen DeGeneres, and Kraft Foods for the rainbow oreo ad, and video stores for stocking "The Last Temptation of Christ", and liberals boycotting Mel Gibsons's sh*tty religious movie, for reasons other than its suckitude, or Dominos Pizza.
That said, if private individuals object that a portion of the money they spend at vendors ends up supporting advocacy groups that they disapprove of, have at it. That is a perfectly acceptabel choice in my book. What is not acceptable (and damn, what just MUST be illegal) is politicos using public policy to "punish" those with opposing views. I think the owner of Chick Fil A is a tool ("we are inviting God's judgment on our nation!") but I hope and presume that he will sue Boston, Chicago and San Fran, if they hold the ban.