I think it boils down to two key concepts, one simple and one complex:
(1) Pool developed and waxed in popularity as a mens' activity done by men in places only men went, and
(2) Places full of only men tend to become inhospitable to women.
Item (1) is pretty uncontroversial and easy to understand if you consider the era during which pool developed and became popular. In the second half of the 19th and first half of the 20th century, attending billiard halls was one of a large category of pursuits that, as a woman, simply were not done. I can't cite sources, but as a sociologist/anthropologist I doubt you need my help in that department.
Item (2) is more nebulous, but in my experience, men act very differently in the absence of women than in their presence. All manner of social graces are disposed of, and it's an unspoken law that a man is not to criticize another man's social graces. A place without women is a place without judgments of a certain type, and thus a place where a man is free to be kind of a jackass. If a small minority of women is introduced, one of two things will happen: the amount of perceived female judgment won't surmount the status quo of machismo and jackassery and the men will go on being jackasses, or the amount of perceived female judgment will be enough to hamper the jackassery and the female presence will thus be resented. In either case, the woman or women will not feel welcome.
Jackassitude aside, there's another effect at play when a female minority enters a male-dominated arena, and that's novelty. Where men might be able to act like normal humans in a situation of 20 men and 20 women, the novelty of one or two women entering a room full of men makes us fall all over ourselves trying to impress, befriend, protect, or seduce. For the women, this is awkward and annoying at best, and quite threatening at worst.
Mitigating item (1) is the fact that there are some pool halls that actually have a quite lively bar scene, and lively bar scenes generally if not always involve a relatively balanced gender distribution. In such places, item (1) doesn't hold and item (2) is therefore irrelevant.
There are also women that love the game and are dedicated to improving and competing, and will put up with the boys' club nonsense if they have to. I think the relative scarcity of these women compared to men who are similarly dedicated to improving and competing has to do with how boys and girls play differently. Whether it's instinctive, cultural, or some combination, little boys compete with each other and battle each other as a mode of play. Little girls in general tend more toward cooperative play. The spirit of matching up and climbing the pecking order in the pool room seems to appeal correspondingly more to men than women, and thus "love of the game" seems to have its own gender bias.
-Andrew
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