As a business owner, I don't believe employees should have the right to exercise their 1A rights while 'on the clock' - since it has nothing to do with my business.
That said, I would never ask employees to pledge allegiance to a flag or honor the national anthem, since it has also nothing to do with my business.
The NFL made the deal with the devil here, so to speak, by incorporating this in the first place. Once again I bring up how stupid it is when businesses wade into politics when it's unnecessary - you will almost always alienate a portion of your clientele.