Because it, the character, is neither male nor female, nor even a true combination of male and female. It is a male soul housed in a female meat sack. It is neither male nor female, except in the context of the external participant's perception of the character in the moment.

If you attempt to address the totality of the character as "he" then you are half wrong, and the same with referring to it as "she". It is the gender neutral pronoun in the English language. The "dehumanization" of using "it" is perception based on the reader's bias.