From FAQ on MLBPA site:
"All players, managers, coaches and trainers who hold a signed contract with a Major League club are eligible for membership in the Association. In collective bargaining, the Association represents around 1,200 players, or the number of players on each club's 40-man roster, in addition to any players on the disabled list."
So any player with a signed contract with a MLB can be in the MLBPA, but only those on the 40 man participate in the bargaining (can vote, etc).