Jews knelt in the Temple. The reason we don't kneel now is that we don't want to equate anything with that. In fact, if a Jew kneels on a marble floor for some reason, he's supposed to put a cloth or some other barrier between himself and the floor. Some people say one should do this even on a wood floor, but we don't require that in Chabad.
We kneel several times as part of the service on Yom Kippur, and once on Rosh Hashana, because that's when it was done in Temple times. When we kneel, we also do prostration, with our heads even touching the floor, which is a total nullification of self, something you'd do in the ancient world before a great king.
At all other times, in place of kneeling, we instead bend the knee slightly and bow the head. Bowing the head shows we are before someone worthy of reverence. The head is the most important part of the body--it's what contains our essence, and we can't live without it. The first person to bow before God was Adam: As soon as he was created, all the animals thought he was their master and creator, and he said, "Let us all go together and bow before God who created us." As for bending the knee, standing upright is a sign of human stature, so we break that when we bow, to show that we are standing before something more important than ourselves.
Rabbi Levi Shemtov
Executive Vice President American Friends of Lubavitch (Chabad)
Judaism is an embodied practice: As the People of the Book, we tend to think of ourselves as living in our heads, but a lot of ritual involves experiencing things through the body. Using our body to designate an emotion--or to propel ourselves toward that emotion--is very Jewish. In services, we bow all the time, and that's to show our submission to something greater than ourselves, to everything we don't understand in the world.
I gave some thought this year at Yom Kippur to whether, during the Great Aleinu--when, at our Sixth and I service, many people kneel and prostrate themselves, not just the rabbi and the cantor--I should encourage people to kneel instead, as a way to connect to the football players who are "taking a knee."
The players also are using embodied practice to make a statement.
But then it occurred to me that the football players are doing the exact opposite of what we do. They're kneeling in order to build power, whereas we kneel in order to give power away, to show our submission to God...