The 23-year-old was criticised in some quarters after opting not to sport a Remembrance Day poppy on his shirt during the game at Everton last week.
McClean was introduced as a second-half substitute in the 3-1 win at Fulham, receiving a mixed response from the travelling support.
"James will deal with the booing. I think it is to do with the issue last week, it's a free choice in this world," said O'Neill.
"James has lived with a lot of things - he's getting death threats too now so that doesn't help."
McClean was subjected to abuse on social networking sites earlier this year after electing to switch his international allegiance from Northern Ireland to the Republic of Ireland.