The purported reason for this action is to stem the rising tide of sexual harassment/violence against women which has accompanied the "Arab Spring."
"...The move is part of its efforts to curb sexual harassment, which is rampant across the country. According to state-run daily newspaper Al Ahram, the No. 909 train connecting Cairo and Alexandria departing at 9am will host the first women’s car..."
Segregation of the sexes has always been an integral component of the Shari'a and the fact that it is now going to be enforced, at least on the country's major rail lines, should not be surprising given the ascendance of the hard-line Islamists such as the Muslim Brotherhood and the Salafis.
In numerous public statements, mostly in Arabic, Egyptian president Morsi has repeatedly maintained that it is his intent to govern within a fully Shari'a compliant framework - so such a move would be fully consistent with his views.
The only credible opposition to Mr. Morsi [the Tahrir Square and other major city "rioters/demonstrators" are largely unorganized and representative of varied and often competing views regarding what "civil government" in Egypt should look like] at this point is the even more fundamentalist Salafis and one can hardly expect their influence to serve as a moderating factor in this matter.
While there may be legitimate concern over the rapidly spreading [and very real] wave of what can only be described as anti-female rage within the Egyptian culture, we believe this move is just another manifestation - a not-so-coincidental, by-product, if you will - of the society's exploding Islamist mindset under the leadership of the Muslim Brotherhood.