The Black Lives Matter movement is a real protest about racial inequality surrounding parts of American society. It's important to recognize this because if one part is treated differently than that allows the precedent of singling out any group for any reason. This is the core principle of the statement "an injustice anywhere is an injustice everywhere."
I have heard people say that they feel Colin Kaepernick is disrespecting the flag and that he should have found another way to protest. Well, that's not how civil disobedience works. The point is to make people uncomfortable until the issue is addressed and resolved. In this way Kaepernick picked the right target. Those complaining need to get over their worship of the flag and recognize that people in this country are being killed in police custody, without an order of execution (which is another rant I will get to at a different time). This is unacceptable all the time.
It further astounds me that people have made this about the American flag. Considering that it's the national anthem that he's protesting, during his taking a knee, I'm not sure exactly how this is connected to the American flag. I'm going to give the benefit of the doubt here, and talk about what the flag actually means.
From a vexillology (the study of flags) perspective it means 13 colonies and 50 states. The colors of the flag are representative as follows White signifies purity and innocence, Red, hardiness & valour, and Blue, the color of the Chief (the broad band above the stripes) signifies vigilance, perseverance & justice. That's what the flag means and nothing Collin Kaepernick is doing is going to change that, but it might change us into living closer to these ideas.
If you want to know more about the black lives matter movement, and alleviate yourself of some misconceptions you probably have about this movement (I know I had a few and didn't realize it) read more here: http://blacklivesmatter.com/11-major-misconceptions-about-the-black-lives-matter-movement/