The main purpose for attending places of worship is to worship, and not to mingle and mix with people of the other gender. This means that we need to keep the atmosphere in mosques and Islamic centres as spiritual as possible. With mixing between genders, this might lead to unwanted outcomes that would go against the ultimate purpose of places of worship.
It is also a matter of convenience for both genders.
This in no way does it mean that females are to be left out of any active participation in programs, or for them to feel marginalised. Rather the opposite. In most places of worship, our sisters are actively contributing to various religious and social programs. However, we know as Muslims that we do not accept "free mixing," and therefore we must preserve the moral and spiritual purity of our environment.
There are times when women must be on one side, and men on the other, and there are times when brothers and sisters can be together, keeping it within the shar'i boundaries of Islam.
And Allah knows best.