Why does FIDE rate women in different category? Has FIDE ever given reasons why it rates woman in different category and organises their tournaments seperately?
First, let's clear up a misunderstanding.  Women and men are rated on the same scale, with the same formula.  A woman with a FIDE rating of 2400 can be assumed to be equally matched with a man with the same 2400 rating.  FIDE merely defines four titles that are only available for women.  In general, woman can and do participate in tournaments against men.  However, there are a handful of tournaments open only to women, including a Women's World Championship.

The reason for the tournaments and titles is obvious: some women want to participate in such tournaments, and some women appreciate the titles.  Chess is filled with reserved tournaments and not-too-prestigious titles of other kinds - this isn't a "woman-thing".  Every club, state, or national championship is a tournament which sacrifices strength and prestige to encourage the participation of a specific group.  The USCF has titles down to "4th Category", a title which requires hardly more than a heartbeat and a willingness to play in at least five tournaments, obviously to encourage tournament play among those still learning the game.  FIDE correctly calculates that having the WGM, WIM, WFM, and WCM provides motivation for some women and encourages them to improve their game and participate in tournaments.  Given that FIDE exists to promote chess among all populations, including women, providing these title is a no-brainer.

Damning women who participate in such tournaments or accept such titles is as ridiculous as complaining that the Canadian National Championship is tainted by the lack of Americans in the field or considering the USCF Candidate Master title to be a farce because it is easier to obtain than the FIDE Candidate Master.  There is no shame or fraud in competing for these titles, as the requirements are well-known and observers can easily understand exactly how much prestige should be attached to them.  Some of the strongest women players may disdain the women-only titles, but there are many male GMs who disdained their IM or FM norms.  You may choose to learn what you want from their examples.