The rules state it benefits the shooter. I believe the reasoning is that:
1. This rule is just mainly to prevent "obvious" fouls.
2. If every close call is against the shooter, how annoying would this game become. It does not progress the game. Example: Snooker (even though I know its not the normal game we're applying it to in this case). The non-shooter can require to have the balls placed back in their original positions and have the shooter attempt the shot again, and again, and again. (assuming each try was a split hit).
So long as a referee, in his best judgement, could not declare it an obvious bad hit, then to progress the game, it would be make sense to give the benefit of the doubt to the shooter. Remember, it works both ways! When this shot comes up for you, this should be beneficial.