I'm not saying whether I personally agree or disagree....here is a rationale however for why punishing "the team" might make sense. If you (the team, the team's coach) know you have a problem player, either rein him in or bench him rather than have him put other people's lifelong ability to walk at risk.
In other words, you are not so much "punishing" the team; instead, you are providing the team with a very strong incentive to police themselves. The rest of the kids on the team "should" exert peer pressure on the problem player, the coach "should" think twice about playing the problem player, etc.
That being said, 3 seems to be too low a threshold for this severe a punishment, given that many of the calls will be arbitrary one way or the other, that's just human nature.