The League Rule Book only covers game play. The operations manual, OTOH, covers how the game is to be conducted.
"The National Anthem must be played prior to every NFL game, and all players must be on the sideline for the National Anthem.
During the National Anthem, players on the field and bench area should stand at attention, face the flag, hold helmets in their left hand, and refrain from talking. The home team should ensure that the American flag is in good condition. It should be pointed out to players and coaches that we continue to be judged by the public in this area of respect for the flag and our country. Failure to be on the field by the start of the National Anthem may result in discipline, such as fines, suspensions, and/or the forfeiture of draft choice(s) for violations of the above, including first offenses."
Two words in the op-man, "should" and "may" are why the players are not being disciplined. Had it said "players on the field and bench area are required to stand at attention, face the flag, hold helmets in their left hand, and refrain from talking" The penalty section would require the word "may" changed to something like "Failure to be on the field by the start of the National Anthem WILL result in one, or more, forms of the following disciplines"
Just clearing that up.