Probably because there're more white skinned people making games?
When you are white and you make a game the bad guy can be white, black or green, whatever fits the story or concept. But for the protagonist, unless you have an specific setting for him, you will go with your standard. That specific can be either having a racial connotation, a gender connotation, a personality connotation...
I mean, it is not rocket science. I'm doing a game myself and my chars will most likely not be dark skinned. Dark skinned people don't play a substantial role in my life, simple as that.
But hey, everybody got the right to be offended, isn't it? Like, Evil Ryu and Violent Ken could be dark skinned because the artist wanted to empower their consumed by an inner fire look of them. Or it could be because they are racists.
Since everyone has the right to be offended, allow me take offense from threads like these.