It's seen as disrespectful because it has always been seen as disrespectful. I promise you if you travel back 10, 20, 30 years and kneel/sit for the national anthem you would receive 99% agreement that it is disrespectful. There are very few things in the United States that you could find so much agreement on. To say that the media is making that up is just false. Again if I want to wave a rebel flag around it doesn't matter if I don't mean any disrespect, many view it as disrespectful and a symbol of hate.
You are correct that the whole point of a protest is to make people uncomfortable and to get people to talk or think about what you are doing. This is a case of the protest overshadowing the cause(s).

