Since helmets are removed and heads are bowed while kneeling, I'm confident prayers are being whispered. And yes, they kneel for Blacks hurt and killed unjustly -- and pray for an end to it.
You have no idea if anyone is praying, but even if they are, they can pray at any time. It is not necessary to disrespect the flag to do that. And no, they are not kneeling for all black Americans. This has only been a protest over police killings. You can be certain they are not protesting the three hundred thousand black babies killed in abortion every year. It's just a political stunt.
I'm not trying to suggest that many of the players don't have sincere feelings about the issues. I don't doubt that, but from the point of view of those who organized this, it is just political. It basically accomplished nothing other than, in all likelihood, helping Harris/Biden get in office.