I remember several cases of people being arrested for making threats against the president, (Not just the current president, but the two previous residents of 1600 PA Ave as well) but for making negative comments? Links please, and something substantial.

Rights infringed? The military was enforcing long standing policy, (The military has a reg for everything, up to and including marital relations with your spouse) the case went to court, the court ruled in favor of having other religious symbols in military cemeteries,case closed. It's the Constitutional process, it worked as it is supposed to. Everyone gets their day in court if needed.