Why ? Now without putting forward any further personal comments, please explain.....
The flag is an American symbol for freedom. Even individuals who chose to protest against it are being patriotic--it's their free right to do so as Americans. Taking a knee during our national anthem was never meant to be a full-on sign of disrespect, which is why the NFL players went down on one knee. Did you read that NYT article written by one of the NFL protesters? Do so, as it explains their gesture.
ISIS doesn't even figure into the discussion. They don't care about our Bill of Rights, nor are they American citizens, nor are they "taking a knee". Their actions show that they are the enemy of pretty much everything except for their own narrow-minded warped world view, so their motivations for burning our flag (which, again, is really really really different from NFL players taking a knee during our anthem) are not rooted in patriotism, principles, or anything that has to do with this discussion. Japanese soldiers during WW2 routinely burned the US flag--it's what enemies do, they burn effigies/symbols of their opposition. But such actions are world's apart from an American black athlete raising his fist or taking a knee.