My opinion is that the message they are sending by kneeling for the flag and the anthem is that the reality of our country is not living up to the ideals represented by those symbols. That's not disrespecting the flag or the anthem, it's admonishing the country to honor the flag and the anthem by being what this country is supposed to be (equality for all), instead of just taking the easy way out and standing for the anthem and feeling patriotic because you do that, but not living it in your daily life.
If you're a religious person, think of it like this. In a lot of churches, the worship leader asks everybody to stand before the music begins. What's happening here is like if one member of the church decided not to stand because he was fed up with the way people in the church act all pious on Sunday morning, and then go out into their daily lives and treat other people like crap. By doing so, he's not disrespecting the worship songs, he's trying to remind people that it's more respectful to what they represent if you actually live it out in your daily life instead of just standing for the abstract representation of what you're supposed to be doing, and acting like that's enough.
