if you're referring to toughness and courage, we don't really have much to go on other than the fact that a male of a species will tend to be bigger and stronger

We don't? Are you saying that we don't study behavior in humans and other species, and can't make observations and predictions based on those studies?

this is not an indicator of toughness or courage

As a rule, bigger muscles aren't always indicators of toughness and courage, but toughness and courage are indicators of toughness and courage. Are you saying that we can't observe these behaviors in humans and other species?

Evolution has made us all pretty good at what we do. Birds are amazing at flying - except the ones that run, and they're amazing at running. If we aren't good at what we do, we die. Wouldn't it be weird if one sex of a species evolved to be physically tough in order to protect his family, but didn't evolve to be mentally tough in order to better handle intense, combat-like situations?

If someone evolved physically to chase and kill prey, wouldn't it be weird if they didn't evolve mentally to be able to better handle those conditions? Especially compared to an animal that never chased or killed anything?

Sex and gender are not the same thing anymore

But sex and gender almost always align, so the distinction is almost unnecessary except for a very small percentage of the time.

these differences were more important to primitive humans than they are now

"Less important" doesn't mean "lesser" here. The differences are the same as they've been for millions of years, because we haven't evolved in a world where hunting and physical confrontation aren't a major factor. That world's only existed for thousands of years. So our brains are still being built for the world where biological differences are important, despite the fact that we don't need them as much anymore.

We are educated and advanced enough now that we know better than to assign arbitrary characteristics to men and women

The characteristics are anything but arbitrary, as discussed above.

anybody should be able to be whatever they want regardless of their genitals

Agreed.

It is unfair and narrow-minded to compare instincts in animals to instincts and gender in humans

We are animals, and despite our consciousness, our instincts drive our motivations and behavior. Look at what we're driven to do as humans. Is it any different than gorillas? We seek food and water, a mate, children, trustworthy friends, a good standing in society. All of that is driven by instinct, and the way we go about it is too. I'm not sure how you're imagining how our brains work, but the chemicals that motivate and reward us are the same as any other animal.

and our survival is no longer based on strength and instinct as much as it is based on intellect and tolerance

Agreed to a point, although "tolerance" was kind of thrown in there. An animal that needs help from other animals to survive won't be very successful if he's intolerant. See how long a lion would last if he was constantly picking dumb fights because he hated everyone and they kicked him out of the pride. Not exactly something that's unique to humans. Intelligence helps a lot though.

The condition of being human calls for us to think beyond instinct and contemplate what is right and good

I agree. But you haven't made a single point towards why it's wrong to point out the differences between male and female behavior.