... Except that they aren't entirely women.. Women are generally more powerful, but that doesn't mean they are the only ones. Besides, look at the advent victory/defeat screens. You'll see men and women.
As said here, women are usually more powerful and so they are the ones that become ship captains, and so they are the ones you talk with on the comms / telepathic link / whatever when you click on a unity and give it orders.
There is probably the occasional male captain but I don't think stardock wanted to go through the trouble of making a % chance that certain ships have male voices and then actually get the recordings of male voices just for that.