Protests take place in as public an area as one can find to draw attention. For these players it is on the field, but it affects the owners' business, and as private business owners they have the right to set rules. They want to be sensitive to the concerns of both their players and their customers.
If I'm the owners I simply don't have teams come out until after the anthem, but also give players time before or after games to meet with reporters about their social concerns.