There are two prats in this situation. Firstly the idiot who threw the flare, and secondly the idiot who came up with the rule of fining the club.
The kind of pea-brains who throw flares and cause violence don't really care about their club or fellow supporters anyway, so fining the club money or points is actually punishing the players and all the law-abiding supporters.
The only way to stop this happening is to identify the individuals and hit them with draconian consequences that not only take away their opportunity to do it again, but also strike enough of a sense of self preservation into their similarly dense 'friends' to make them think twice too.
Of course, this task isn't easy and rests primarily with law enforcement, but that's why the authorities go for the easy and symbolic option instead. Absolute waste of time.