Page A62 of the NFL Game Operations Manual which has not changed since 1978.
It also reads that, "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.”
The NFL handled this wrong because they are not run by basic business/capitalist principles. They are a monopoly who (in most cases) receives public funding for their stadiums. They get their money up front for the seat licenses and season tickets. The TV deal runs until 2020 and, again, the NFL will get paid and the fans have little recourse. A normal business, especially a mom and pop, would be out of business the following day if their employees conducted themselves in this manner and the business owners/employers approved of that conduct (which the NFL did).
At this point, the issue with the players, at least to me, has become secondary. The NFL came out and condoned it and even supported it. Quite frankly, there's nothing wrong with that. They are the employer and that it there right to run their business as they see fit but they've told their customer base where they stand on these issues. People can continue to tune in or tune out. I've tuned out with he exception of the watching Cowboys but I wasn't too thrilled with the organization taking a knee prior to the anthem. This tells me where they are and where they stand (no pun intended) as an organization. After 45 years, my interest is waning.