Scott was suspended indefinitely by the NHL on Thursday pending a disciplinary hearing one day after his blindside hit to the head of Boston Bruins forward Loui Eriksson.
Cherry, speaking on the Coach's Corner segment of "Hockey Night in Canada," said Scott was under pressure to make a hit due to his limited ice time.
"Now here's a story. He sits there for 55 minutes. He's put on the ice. He's got to do something. He's got to do something or he's going to be gone. ... It's so unfair," said Cherry, who added he was once in the same position as a player who had to fight or not play at all.
Scott, who was issued a match penalty for charging, and was ejected after the hit on Eriksson in the neutral zone, played just five minutes 15 seconds in the 5-2 loss to Boston.
Cherry pointed to the 31-year-old's average time of ice with Minnesota in 2008-09, which was 9:14 in 20 games under coach Jacques Lemaire. The next season, Scott averaged 8:36 in 51 games.
The hockey commentator then turned the blame on Sabres coach Ron Rolston.
"He's got to play John Scott. Lemaire did it, Hall of Fame guy did it, and that's the way it should be," said Cherry.
Eriksson meanwhile is out indefinitely with a concussion.