George, there was a man living in Montgomery, Alabama and flying the United States Flag at his home from what I can remember. Needless to say he was very unpopular with many of his neighbors. I can't recall if he was ever formally charged with treason but he was hanged during the war but I can't recall if it was a lynch mob or legal authorities.
I would image some folks in the border states may have been charged for treason. West Virginia comes to mind. The South took many civilians as prisoners during the war and I would lean toward some of them having been charged with treason.
One of the Andrew Raiders on the Great Locomotive Chase was a civilian with the surname of Campbell. Since he was wearing civilian clothing he may have been charged as a spy?