Running in itself isn't bad. Running leads to improved cardiovascular fitness and improved muscular endurance. How running is used it the question here. There are three basic ways a coach can give feedback to players about their performance in both practice and games. These are positive reinforcement, negative reinforcement, or punishment.
Positive reinforcement is feedback, which stimulates the re-occurrence of a given behavior.
You know you will get a pat on the back when you make 10 shots in a row. Negative reinforcement works the same way only there is a pre-stated consequence when a particular undesirable performance occurs. For example if the coach tell you, we will run 10 lines if we lose to this team, it is negative reinforcement. The onus to avoid this action lies with the team. If you perform like they are capable and win, there is no negative consequence.