Welcome to Unions 101. The NFLPA bargained and signed an agreement that applies to all players. For all of the benefits that the players have earned over the past 50-60 years (free agency, salary floor based on revenues, reduced training schedules and workloads, rookie wage scale, etc.) they have had to concede other points to the owners (franchise tag, salary cap, rookie contract lengths, etc.). In a business where a union is involved and gets you benefits that you wouldn't normally receive in a pure capitalist system, you also have to give something up.
I just don't think workers have or have ever had the same bargaining powers as management. Most important worker rights in this country had to be legislated.
Wait, you think the ability to have free agency is a benefit that the players should be happy they received?