See I don't get this. How is kneeling not disrespecting the flag and the national anthem when that is the customary way to honor the flag and the national anthem?
First, let me say that I love your avatar
To your question: I feel that kneeling is a respectful gesture in general, and in CK's case, has religious bearings.
Also, kneeling isn't listed as being disrespectful to the flag in the U.S. Code. Although several things are that I see on a daily basis that I don't see people raising much fuss over.
§8. Respect for flag
No disrespect should be shown to the flag of the United States of America; the flag should not be dipped to any person or thing. Regimental colors, State flags, and organization or institutional flags are to be dipped as a mark of honor.
(a) The flag should never be displayed with the union down, except as a signal of dire distress in instances of extreme danger to life or property.
(b) The flag should never touch anything beneath it, such as the ground, the floor, water, or merchandise.
(c) The flag should never be carried flat or horizontally, but always aloft and free.
(d) The flag should never be used as wearing apparel, bedding, or drapery. It should never be festooned, drawn back, nor up, in folds, but always allowed to fall free. Bunting of blue, white, and red, always arranged with the blue above, the white in the middle, and the red below, should be used for covering a speaker's desk, draping the front of the platform, and for decoration in general.
(e) The flag should never be fastened, displayed, used, or stored in such a manner as to permit it to be easily torn, soiled, or damaged in any way.
(f) The flag should never be used as a covering for a ceiling.
(g) The flag should never have placed upon it, nor on any part of it, nor attached to it any mark, insignia, letter, word, figure, design, picture, or drawing of any nature.
(h) The flag should never be used as a receptacle for receiving, holding, carrying, or delivering anything.
(i) The flag should never be used for advertising purposes in any manner whatsoever. It should not be embroidered on such articles as cushions or handkerchiefs and the like, printed or otherwise impressed on paper napkins or boxes or anything that is designed for temporary use and discard. Advertising signs should not be fastened to a staff or halyard from which the flag is flown.
(j) No part of the flag should ever be used as a costume or athletic uniform. However, a flag patch may be affixed to the uniform of military personnel, firemen, policemen, and members of patriotic organizations. The flag represents a living country and is itself considered a living thing. Therefore, the lapel flag pin being a replica, should be worn on the left lapel near the heart.
(k) The flag, when it is in such condition that it is no longer a fitting emblem for display, should be destroyed in a dignified way, preferably by burning.
