The second reason is that having a female protagonist changes the entire meaning of the story. Consider Pierre Menard, author of Quixote (https://en.m.wikipedia.org/wiki/Pierre_Menard,_Author_of_the...), which discusses how the particular context of the author effects the meaning of the work.
Wikipedia had an excellent article about gender representation in video games https://en.m.wikipedia.org/wiki/Gender_representation_in_vid... . One part of the article notes:
> 60% of girls but only 39% of boys preferred to play a character of their own gender, and 28% of girls as opposed to 20% of boys said that they were more likely to play a game based on the character's gender.
So it may not matter to some people, but it matters greatly to others.
To go deeper into the problems of story telling in games, see Jonathan Blow's Conflicts in Game Design Talk.
https://www.youtube.com/watch?v=mGTV8qLbBWE
But as for actual story telling games with female protagonists, go back to King's Quest IV: The Perils of Rosella. Designer Roberta Williams said a lot of interesting things about it, like how it was more uncomfortable designing deaths for her, and how she was worried there would be a fan backlash to playing a female character (but never happened).
Hell, since I mentioned both Jonathan Blow and King's Quest, somebody just did a big ass Sierra retrospective applying Blow's talk to Sierra games, examining both why Sierra was able to successfully do story telling games for 20 years and how they differ from modern adventure games. Highly recommended.
https://www.youtube.com/watch?v=wua96SI6SBE&list=PLPAVYgFfed...
However many many people see video games as inserting themselves into a story and if the main character is sufficiently different from themselves this simply does not work well, so they avoid games with protagonists that have certain traits (gender, age and more), which creates financial pressure on game companies to target the most profitable demographics, which in turn often has the result of excluding less profitable demographics.
Thus the struggle between companies trying to make a living and under-represented audiences trying to become represented.
Further reading:
http://www.itinthed.com/16328/what-taking-my-daughter-to-a-c...
https://en.wikipedia.org/wiki/Nier_(video_game)#Development (second paragraph)