Skirts and pants as being female vs male dates back to the Victorian age, although prior to that as well. It was just more expounded on during this time era. Skirts were to emphasize a woman's, 'feminine qualities', meaning her daintyness and fragility. A woman would need a man's assistance to help her cross a puddle on the street to ensure her skirt didn't get wet. It just fed into the stereotype and notion that women were dependent on a man to protect them. Plus its all about gender roles. Men are men, women are women, and that necessitates into their dress. Men don't wear skirts (of course, unless they are Scottish, but they are called Kilts, and that, of course is acceptable) and women don't wear pants.
Another reason to not wear pants is to avoid showing the female form, as a sillouette. Pants would show the hips and the female reproductive areas more so than a flowing skirt....and to showcase that area would be vulgar. Eventhough a man can wear pants and have his areas, 'exposed' in that form, it takes the shape of a phallus and that showed dominance and power. Eventhough their pants werent the tight jeans of today, it still was considered form fitting.
It wasn't until WWII that pants for many women became an issue of practicality, since they had to join the workforce for the first time, skirts just wouldnt do in a manufacturing plant or at the store. And then Kate Hepburn being a strong advocate for being feminine AND wearing pants during the 1940s really helped shape the idea that pants are unisexual and that being a woman doesn't mean only wearing skirts.
Reminds me of one of my theses in college.