Disagree in regards to ending the anthem playing.
One reason to play the national anthem and a reason to honor our national flag before a very large sporting event - is to promote emotional solidarity and unity. Same reason for fly-by's .
If there was enough emotional solidarity (unity - a.k.a. we are all in this together) in this country, there would be less issues - like the very one the player is trying to make a statement about by raising his fist.
A country without enough national unity is a weak nation destined to be conquered or otherwise destroyed by other nations run by evil tyrants. In the grand scheme of things promoting emotional pride in your nation is a good thing assuming your country isn't being ran by an evil tyrant. And it is a constant reminder of the past that you are doomed to repeat if you forget about it.