This is an established function of the player's union that goes into effect when a team is denying bonus payment and is not affected by Hernandez's current legal position. The contention of the union is that the workout bonuses were scheduled to be paid before Hernandez's release from the organization, so the bonus should not be impacted by the player's arrest.
Hernandez was arrested in June for the murder of Odin Lloyd and is currently awaiting trial. The New England Patriots cut the tight end shortly after he was arrested, releasing a public statement voicing the team's "disappointment" that one of its players was arrested.
The $82,000 workout bonus sets the table for a potentially larger fight between the Patriots and the NFLPA. Hernandez was due a $3.25 million roster bonus in 2014, and it remains to be seen whether the union will file a separate grievance in an attempt to recover some of that money.