Target minutes allow you to provide a range of minutes you'd like to see each player receive during a normal game. Obviously, in close games or games which go to overtime, you're more likely to see your starters receive more playing time than your backups and vice versa.
In addition to providing a range of targeted playing time, you can also designate players to a 'mopup' role. This means that they'll play when the game is out of hand (or in case of emergency situations due to fouls, injuries, ejections, etc.). The other option is to designate a player as 'rest'. This option is only available for players who were injured and are not yet 100%. They will NOT dress for the game.