Freedom doesn't mean that no one can question our actions or intent. Freedom doesn't mean that we can't or won't be accused of wrong-doing. Freedom means that there are checks and balances to aid us when these things happen.
Police don't single out people with cameras. They single out people across the board. It's not like they are out there hunting down everyone with a camera or slapping the cuffs on everyone they see with a camera. I've been spotted with a camera dozens of times and never has a law enforcement agent ever questioned me, let alone yelled at me or slapped cuffs on me.
That article seems to hint at the police having told the guy to go inside prior to having cuffed him. The quickest way to find yourself in cuffs is to blatantly defy the police and ignore a request to go inside. I wonder if the guy went inside to retrieve the camera phone after having been asked to go inside. I can understand how that might prompt the police to place the person in custody.
Lee Shively makes some good points as does df cardwell in mentioning how the typical person may react when a stranger is caught photographing them in an awkward moment.