Well, I do agree, if its not done right it could suck, but if there is a penalty slider that works, players could set it to their liking.
Also, it should vary game by game, and team by team.
Players with alot of undisciplined players and coaches would have a better chance to incur more penalties than disciplined teams.
Also, some games would be different than others. Some games may get called more strictly.
Penalties are frustrating in real life, so they should be in the game as well. Not to the point it makes it frustrating to play, but in a football SIM, that element needs to be there.