The protests have zero to do with disrespect for the flag or anthem or lack of patriotism. The athletes and many others have said repeatedly they have respect for the flag, for the anthem for the military and our country. So much respect that they actually believed they have the right to free speech and expression and can use their platform as athletes to promote change peacefully.
According to our Constitution and many court cases over our history, they are correct.
According to the legally binding and collectively bargained rights as NFL players, they are also correct. They also CANNOT be fired for such protests nor should they be. That would be completely outrageous in the United States in 2017 to have happen.
Furthermore, the President CANNOT tell people what to believe or do and certainly has no right to tell a private business (The NFL) how to handle their employees or run their business. In fact, that would and should lead to furious backlash by the very conservatives who so zealously guard their rights as business leaders. Imagine if anyone has the gumption to tell Trump how to run his real estate business? That would be wrong especially from the President of the country.
The protests have always been to raise awareness and hopefully encourage change in our criminal justice system in regards to police brutality and minorities being killed due to bias, poor training, lack of community-police relations and other reasons.
Those are very valid reasons to protest and, if Trump and his cronies spent half the time they do on lining their own pockets on the public dime and damaging our Republic, on working toward solutions to help mitigate the criminal justice problems and the inequality that exists all across this country between the wealthy and poor, white and black/brown/red etc. we might be able to actually improve our society and world together.
Trump unfortunately has shown he clearly is a bigot, one who does not care about anything except power and his own ego and is eager to continue playing on our divisions rather than working to unite all Americans. Not just the ones he feels comfortable with or believes are "worthy".