There's a thread about bullying on sherdog right now that parallels this nicely.
School administrators claim they care about bullying, but they don't. The only thing they care about is limiting the number of violent incidents to as few as possible. For them, a kid who is bullied for a lifetime is a better statistic than if that kid who is bullied sticks up for himself once.
Its more about the confidence that doing something you are good at provides than learning to fight. The difference between kids that were bullied and those that were not when I was young was rarely one to do with fighting ability, or a willingness to end it in a violent confrontation. Protecting kids from bullying is more about building self esteem, which any sports training (including martial arts) is good for.