The "US flag" part of the issue is a red herring. The article states that the rule applies to any flags or religious symbols. The real issue isn't "Anti-Americanism"-- it is allowing your freedoms to be limited by Home Owner's Associations and property management. The rules were probably laid out in the contract that he signed to live on the property, and he signed it anyway.
Edit-- an article updating the story:
http://www.wbay.com/Global/story.asp?S=12556803