They live in a pagan society. Of course their gender roles are different. They have female gods not just one, singular, male God, who tells all other human males that they're superior and to write books to the fact.
In BSG they had a female president and didn't even blink at her gender.
Admiral Cain was Admiral of the entire Colonial fleet. In the US we're not even allowed to have gays in the military or women in combat jobs.
The Mother is the leading religious authority in the Church of the One God. Catholics won't let women be priests.
According to the Athenian religion on Caprica, you're allowed to have polyamarous marriages. Not only that, but a woman is the dominant person in that group's relationship. Granted, they're a sleeper cell for a terrorist organization, but the point still stands that they have what Lacey called "Multiple Marriages."
Look at Sam Adama. He's gay, married, and in a high position of organized crime. Imagine a married gay guy out in the open in today's Mafia. The Soprano's (IMO realistically) portrayed one gay mafioso and what happened as a result of his being gay.
I could go on, but I've run out of major examples.
Well, there was that whole Baltar female harem thing.