The Premier League outfit decided to wear special edition shirts for their 2-1 defeat to Everton on Saturday but McClean decided against donning the emblem on his chest.
"This is his choice, the mentality, the habit," said Trapattoni. "I think it's a personal choice and obviously I will defend the player. Maybe it's not over until now, the situation with the Irish people, the north and south people."
McClean was brought up in Derry, which had six people killed in the 1972 Bloody Sunday massacre.