I don't know what Trump thinks on the subject but just because one defends the rights of others to demonstrate how they want doesn't mean they agree with it. I do not support the new book that came out saying the Second Amendment is about anti-blackness. However it is the author's right to publish such lies and if I truly support freedom I can not order such things to be prohibited and banned. That does not mean that I must believe it and accept it as fact, I can call out the lies.
Likewise with the flag, because of freedom of expression, they have a right to wave it peacefully if they wish. But it also means I can think of them as I choose fit. Do I like it, no. Do I agree with it, no. Do I support it, as long as they are peaceful I don't really care. If they want to go into battle with it I might just decide to avenge my ancestor who was killed by cowardly confederate raiders.
In short it falls into the category of I don't agree with what you say or do but I support your right to do so. Obviously there are exceptions, you can not harm others. And some greaseball flying a flag is not harmful. I suppose you can say it might traumatize some people but then some veterans and families of fallen soldiers might feel traumatized when they hear people say allahu-akhbar. Is people to be prohibited from saying that? Where do we draw the line with offensive stuff?