Well, ancient Greek mythology stems from a blend of Minoan Crete and Indo-European tradition. Minoan Crete revered women much more highly, with the famous statues of the snake goddess. The roots are also seen in the transition in the Greek mythology from feminine gods (Gaia being the origin) to male sky gods in Kronos, Ouranos, and finally Zeus and the Olympians. It is also important to note that Zeus had feminine qualities, with him eating his first wife Metis and giving birth to Athena and, later, Dionysus (I use giving birth here loosely).
Essentially, what I am getting at is that at its roots, Greek mythology started out as being more feminine (and wild, in Greek thought), and with the spread of the Indo-Europeans become more masculine (and ordered, in Greek thought). There is also evidence in Athene existing for quite some time, with tablets being found in Knossos with her name inscripted on them (though more research does need to be conducted to state anything positively). However, that could be evidence of Mycenaean invasion of Crete following the eruption of Mount Thera, as the language transitions from Linear B tablets to a primitive form of Greek.
I digress, to answer your question again, Greek mythology has its roots in a more feminine and egalitarian society, and their religion reflected that.
Sources:
Feur, Brian
2004 Mycenaean Civilization. McFarland & Company, Inc., Publishers, North Carolina.
Mee, Christopher
2011 Greek Archaeology. Wiley-Blackwell Publishing, Chichester.
Palmer, Leonard
1962 Mycenaeans and Minoans. Faber and Faber, London.
Though athena had female form she was not necessarily seen as female. In Aeschylus' play 'The Furies' Athena says that since she was born solely of Zeus (since she exploded out of Zeus' head rather than being born) that she is male in substance. This would explain why athena's provinces, war and victory, are notably those that Greeks would associate with men.
It's also likely Athena worship (or worship of a precursor to Athena) is very old and predates the especially sexist institutions of ancient athens. Given this athenians were likely trying to fit an old god to new way of thinking. By making Athena a male in female form, the athenians could comfortably worship a woman without rewriting their theology.