Hmmm.. very interesting question especially now that Sammie raised this issue. What I find surprising is that when I flip through my Oriental and SEA story shelf I see the other trend going on, the protagonist losing the father at a very young age, and I have a hypothesis as to why protagonist are usually depicted as being orphaned on some way or another. Allow me to elaborate.
In modern day Western culture, the value society emphasises is on individuality and knowing one self. Biologically, a mother is the nurturing force, seeking to bring the best out of her children to the child's potential. This coincides with the Western creed of individuality and know thy self.
In modern day Eastern culture, the value society emphasises as we have for centuries remain discipline and working as a team. Biologically, a father is the force that brings this discipline about and also reins the offsprings in line.
In a normal family, the nurturing aspect of a mother is balanced with the law aspect of the father. Therefore, the child has the best of both worlds.
However, lacking one, the child is in trouble. In Western society, where individuality and personal growth is emphasised, lacking a mother is seen as lacking the nurturing force that allows this to happen. Therefore, for a person to develop this trait in the absence of a mother's support will require a near "heroic" and "self directed ability". This adds to the drama of the story as here we have a person, crippled, chained who by his or her OWN means break through that shell and ascend the path that once he is found wanting.
In Eastern society, where discipline and teamwork is emphasised, lacking a father is seen as lacking a the reining force. The hero is therefore viewed as a raging, charging bull, whose strength is uncontained, lacking societal care. Only when the hero reaches to the collective that he grows to care for society and enforce discipline unto himself, lessening his individuality and extending himself out to the whole, hence ascending the path of where once he or she is found wanting.
It is, in my humble opinion, the growth and struggle towards the innate ideal of society that matters. Removing a parent seen as essential to create a child worthy of that ideal means basically the hero has to do it on his own. This adds depth to the story as it means the hero is growing from incomplete to complete, all by his or her experience and effort!!