[source: American Muslim Women, p. 

MEN ARE SEPARATED FROM WOMEN IN PRAYER TO MAINTAIN MODESTY
Men and women worship in separate sections to avoid physical contact between 
male and female bodies, as congregational prayer requires that worshippers 
stand, bow, and prostrate in tight lines as if they were one unit. Arms, thighs, 
and feet necessarily touch, a condition of prayer expected to engender a sense 
of solidarity among worshippers. This symbol of unity, however, could easily 
cause discomfort if genders were mixed in prayer lines, women's thighs touching 
those of male strangers. Many Muslim women and men offer this rationale in 
defense of their gender separation.
[source: American Muslim Women, p. 171]

MUSLIM WOMEN DO NOT VIEW GENDER SEGREGATION IN PRAYER AS BEING ABOUT MALE 
DOMINATION, BUT ABOUT KEEPING WANDERING EYES HONEST
In some mosques, men and women share the same prayer hall without any partition 
or curtain dividing them. In this case, women usually pray behind the men. Most 
hadith reports indicate this as the gender practice that the Prophet Muhammad 
endorsed in his own mosque in Medina. Many mosque participants support this 
practice not only because of the reported sunnah but also because they view a 
separate women's section in the rear as the most logical gender arrangement. 
Instead of viewing women's position in the rear as a symbol of men's ontological 
superiority over women, as many non-Muslim visitors interpret it, many Muslim 
women prefer this arrangement because it prevents men gazing at their elevated 
rear parts when they prostrate.
[source: American Muslim Women, pp. 171-172]

ALTERNATIVE ARRANGEMENTS FOR MEN AND WOMEN IN THE MOSQUES
A second arrangement, however, removes this appearance of gender hierarchy. In 
this less common setup, men and women pray alongside each other, men on one side 
of a curtain or divider and women on the other. Women occupy the front, middle, 
and rear prayer rows on their side, as men do on theirs. Supporters of women's 
rights increasingly advocate these two possibilities: (1) women worshipping 
behind men in a shared prayer space or (2) women praying next to men in an 
adjacent section. 
[source: American Muslim Women, p. 172]