In my experience, I've found that applying the Golden Rule and "seeking first to understand" generally takes conscious effort and practice... and it's also my assumption that I'm not the only one on the planet like that, seeing as how Steven Covey's "7 Habits" book spent 1/7th of the book on developing empathetic habits.
I don't really know about cognitive emphathy though. Logically, I can understand why someone is upset after they explain it to me, but I normally can't pick up on something until its too late.
This happens to everyone. It's part of normal social growth & development to have your brain wander and suddenly realize one made a faux pas (or figure out the truth about an old situation).
If you understood ASD better then you would realise that would come across as offencive.
As for golden rules, well there are always exceptions to any rule. Getting a job in IT involves convincing a bunch of HR people who know nothing about IT that you are best for the job. That would be the issue stopping most ASD(Autistic Spectrum Disorders) from getting the roles, and startups are just too dynamic and change to quickly for most comfort zones, let alone somebody with ASD.
As for empathy, it is such a open area and yes I'm sure we all learn, still I know if I kick somebody in the bollocks then even I know how that person is feeling ;(
It is often very easy to do a deep kind of empathy, where you focus a lot of energy into running a full simulation of another person in your head. This is often much easier when the person you're simulating is similar to you (e.g., on the spectrum). It takes energy, and it's really hard to parallelize, that is, I can't easily deeply empathize with a dozen people at once.
What a lot of normal people seem to be good at is a doing a first-order approximation of other people's intentions and motivations, a shallow type of empathy if you will. And perhaps it's just that if they're interacting with "normal" people, they can make a lot of assumptions that don't hold true for Aspies.
That being said, there are a lot of good strategies I've learned on how to make chit-chat with normal people and "flow" conversation -- I explicitly had to learn it as I was not born with that package pre-installed.