This is a very good question! I don't believe for a minute that men have some innate capacity for chess that is lacking in women. I think it's a cultural thing - but that's about as deep as I can go on this topic!
Why Are There Women's Titles in Chess?
It may have started as a cultural thing but really I think women go along with it as they earn money alot easier by not having to play men of the same standard, the playing field is reduced.
All credit to Judit Polgar for not taking this easy way out and earning her rating and prize money by competing against men. I also think it's likely that there would be more strong female players if they actually played like Polgar and earned their way like the men do by pushing themselves against more and stronger players.
Given that chess is not a physical activity, where men would have certain natural advantages, such as strength, that could make for an uneven playing field, why does chess offer titles like the WGM (and are there other gender-segregated titles/events)?
Does that suggest that women are held to a lower standard and that they are inferior? Is there any controversy over gender distinctions in chess?