It's a product of sexism inherent in modern globalized culture, heavily influenced by Western cultural expectations. Where no gender is obvious in a given medium, the male gender is typically assigned. In order to be considered 'female' there usually has to be a conclusive indicator towards female gender. In rock-art archaeology, for instance, it was commonplace to assume that a given humanoid figure was male unless there was specific indicators to the female gender of a motif (such as genitalia or hair styles) However, humanoid figures with no distinguishing *male* characteristics would still be assumed to be male by default, instead of going by distinguishing male characteristics.
In the modern age, traces of this can still be seen all around us (although we are getting better) Look at a crosswalk sign. They often have two basic figures on them, indistinguishable except that one of them will have a skirt. The 'male' figure has no features that flat out distinguish it as a man, yet culture assumes that it will be recognized as a man, because the man is 'default'.
In video games, it is a similar mentality. Think about all of the 'canon' characters from video games that allow character customization. Mass effect? Male. Dragon Age? Male. Baldur's gate? Male. Kotor? Male. Saint's Row II? Male. Fable? yep, that's a man on the cover of every single game. Just about the only exception to this rule I can think of is KoTOR II, but there are many, many more examples that merely prove the rule.
It's an unfortunate aspect of the culture we live in, as I would like to see more 'canon' female leads to games, esp in games that allow the character to be either gender.
