That's a really good question.
I really don't know... but we can always make a guess.
Let's see...Blue always stand for quality, pedigree, stability and upper class. Also a sign of strength.
Blue chip (solid companies), blue label (distinction), blue blood (aristocracy), blue ribbon (championship), true-blue (trusty, faithful), etc.
Since solidity and championship (which in those days usually mean superiority of muscular strength) usually are qualities found in men, as is the quality of being faithful to the family line. (Females take the surnames of their husbands and move away from their parents and roots).
Probably that is why blue stands for male or masculinity.
Red... not sure... maybe because in a color wheel, only yellow and red remain on the other side of blue... red came to symbolize women because women undergo menstruation (giving red?)? Perhaps so. To be red would be better than to be yellow... since red has a more healthful connotation.
Also red represented health and vigor... an important thing for women since they are vital in any society for the purpose of childbearing.
And.... pink is just a softer red. Simply a diluted red by adding white. So... it could mean... a more child-like or less potent form of female-ness. And since women like to be forever young... and if pink meant young women... of course they like it. You can see... women, as they grow into more mature images of themselves, begin to use RED lipsticks, or nail polishes, etc. Because they feel their own woman-ness. Girls on the other hand, those young ones or those who like to play flirting.. like pink. Then.. possibly progress to red in a stage of their lives. I have seen this happening with women myself.
On the other hand... men are encouraged to grow.. to be strong, etc. So a diluted form of male-ness, blue diluted by white... is not as popular to men as pink is to women.
Given time... and people... and culture, shake them together and there you have it.
Perhaps that is why after years and years of culture, blue became men's color and pink, women.