This goes along the same line as why don't more women choose STEM fields? I've never really understood why these questions come up. The answer is simple, it's not what the majority of them like. We don't complain that the majority of nurses are female. We don't complain that the fashion industry is heavily slanted toward females. We don't complain that the majority of construction work is males. The USA is a free country and when given absolute freedom females choose the fields they like. Not the ones we want them to like. That's a very important distinction. The same is true for gaming, and if you want to lump it in, American competitive sports as well. Just like most males don't choose fashion, and don't really understand what the hubbub is about, many females feel the same way about football. That's perfectly fine and understandable.
So the answer to your question is simple: By choice. We chose to become the audience, women chose different endeavors. The market formed around us, because that's what free markets do, they find an audience and cater to it. So you can listen to the doom and gloom until the end times, it won't change the fact that when given the freedom to choose, what we call "gaming"(although should probably be termed traditional gaming) is not what women want. Quick games on the phone during commutes, downtime and/or breaks though? Whole different story.
In short, they just aren't into it. That's not a problem, much like which gender chooses which job more, it's a non issue. Gaming doesn't do anything to actively discourage females, and almost every effort made to entice them into playing has been marginally successful at best. Gaming is a business and you can't ask them to continue trying to support an audience that just isn't very interested in what they are offering. Mass effect is a perfect example of this, many males will argue Femshep is the better Shepard, yet only about 18% of the playerbase even tried femshep and that includes the males. From a business standpoint, was it worth it to have femshep in there? Probably not, yet they did it anyway. Kudos to Bioware for the effort, I certainly appreciate it, but if a game comes out that doesn't, I certainly understand why.
Women will like what they want to like, not what we want them to like. All of us(well all of us who are sane) would welcome them into gaming, but if it's just not their thing it is what it is.