Because the focus became what he was doing and whether he had the right to do it, instead of why he was doing it. He didn't create that misdirection.
Had people just asked the deeper question "why is he kneeling," or just said "fine, kneel," this may have been lead to a much needed and meaningful discussion on race relations in this country.
It is not that cut and dry. It very well could be a first amendment issue if a private sector employer violates federal laws, as well as various state or local laws designed to protect and/or promote free speech, anti-discrimination, whistle-blowing, and labor conditions (for example). Additionally, there is the question as to whether those owners and their teams lose that private sector protection when they accept money to build those stadiums from federal, state and local governments, and receive government tax-breaks. To what extent do they become government actors and stand in those shoes? It is a sliding scale and clearly the NFL felt at risk or they would have hidden behind it through summary judgment.