This is all true in real life, but in a fictional story, if the setting implies that women /aren't/ necessarily the weaker sex (due to political traditions or some equalizer like magic) then I don't think that a heroine is necessarily inclined to be more cautious or afraid of rape. Also, some women are naturally very atheltic and muscular, (I'm thinking of some of the athletes I knew in HS), and I don't think they went around with a higher sense of caution than their male counterparts.
I'm sorry that you had a lot of bad experiences in Academia as a female, but I think you'd be surprised at how the climate has changed since then. I majored in math (graduated in 2007) and was never treated as lower than a peer to my classmates (75% of which were males). I was treated with equality in all my classes, too, not just Math. But then again I didn't foray into CS much. I took discrete math and was one of the three or so people who had thier book open and could therefore answer the prof and interact in discussions, so I don't know for sure if /that/ was why I was treated equally or not. In any case, I like to think that the sexism of even 10 years ago has abated quite a lot.
LOL I graduated last year..... but anyways
I would NEVER say that women are the weaker sex. I just think that men and women, either by virtue of society or physicality have different strengths and weaknesses which in turn change the way each genger reacts to certain situations. (not bad or good, just different) The only way to write a woman or man realistically is to take these into account.
A character should be one gender or another for a reason beyond being bed buddies, so if an author chooses to make the main character a woman, why did he/she make that choice? If the gender of the main character doesn't matter, why not write them so they have an ambiguous gender? (actually, that would be kinda fun to attempt...)
I think maybe reading up on the psychology of gender would be useful:
http://www.psychologytoday.com/basics/gender(I would stick with actual psychological research and stay away from feminist sociological papers...)
Women are smaller and have less muscle mass than men. Of course this is not 100% the case, but in general this is true. Being smaller has an affect on the way you react to others. Humans have an instinctual fear/caution about others who are larger or seemingly more aggressive than themselves. This is true for men and women. BUT since most women are smaller than half the population (males), this affects their psychology more than a shortist man who is still taller than some men and most women. (my BF is 6' 6" and all my freinds were afriad of him before they got to know him... ><) On the opposite side, a really large man may behave overly friendly and gentle (big teddy bear) in order to better get along with people, or a really tall man may try to use his size to intimidate people when really he hates to get into confrontations.
Then building upon that, you could say that because people have these tendancies about someone with a particular physical attribute, a stereotype or even cultural standard was created so that most people will see a woman as way less threatening than a man, and women will have to be overly aggressive to intimidate others. NONE of that has anything whatsoever to do with actual power, but percieved power. A small woman may very well be a great warrior, but people upon first glance will still fear the big teddy bear first.
If in your fantasy world, women are bigger and stronger than men, you STILL have to take into account that women carry pregnancies, breast feed (and hence have a child nearby) and possibly menstruate. (lots of people pretend this doesn't exist...LOL) This matters because menstruation and pregnancy make a woman more physically vulnerable and also makes her have to rely more on others. Having children nearby means they need to be more cautious. In preparation for this, even as younger kids, females are are pushed to be more social and have closer ties to their friends (which can also cause lots of drama...). Female relationships are nothing like male ones (like sister/sister or friends, etc) The reason this is important is because a big, stronge, powerful woman, no matter how powerful and undefeatable, is still at some point in her life vulnerable, wereas a big stronge powerful man may not have limitations on his physical prowless or percieved strength until he gets old or really sick.
You could certainly have the guys giving birth, but then you've pretty much made women into men with breasts....
I guess that my arguement is that gender does play a big role in how men and women behave and react to different situations and also how others treat them. No matter how egalatarian a society is, there will be differences due to this. I'm not saying this is good or bad, but gender deffinently shapes how a character behaves and how a character should be written.
The best advice I could give on checking to see if you've written a man or woman well in a work, is to write some paragraphs of the character doing things, and take away all gender ques like he/she and male or female names. (sam, alex and lee are all pretty gender neutral) Then have someone else read it. Most people will be able to say what gender they think the character is. Try doing this with a favorite book in which you think the genders are well written. Its a pretty interesting excersize.
Just for fun:
If I were argueing that gender is a social contruct and sex doesn't affect behavior, I'd bring up transgendered persons who are male or female bodied but feel they have a different gendered mind (but that also brings up the question of what makes a mind male or female?)
I would also point out differences in women between cultures (japanese women and american women are one of my favorite contrasts) Japanese women are not as outwardly emotional and japanese men do have close ties to each other.
I think this is just really interesting:
http://en.wikipedia.org/wiki/Breeching_(boys)
the breeching of boys but not girls would have probably had an effect on girls growing up at that time (the change of dress was a special event for boys, and calling a man unbreeched was an insult)