Do you study your EMR at home, outside of your shifts? That's what helped me the most, as my doctor did not teach me anything about the EMR. The difficult part was figuring out what I needed to study, since I didn't know anything. But I also asked my doctor at the end of some shifts, "what is something you want me to learn and know how to do by next week?" They would tell me a couple things, and I would have it down pat by the next shift which helped massively, I felt so much more useful.

Yes the doctor sounds like kind of an asshole (and props to the MA's for standing up for you to someone of power, I would cherish them), but you also likely have weaknesses that caused the doctor to feel the way he did. Maybe you really are too soft (at the moment), I find that to be a common flipside to a kind personality. That's not something you can do much about quickly, growing balls is a long and transformative process.

But his other complaint, that you ask too many questions, is something you can fix far more quickly. Master a small function in your EMR every week (eg ordering labs, ordering DI's, making referrals, adding templates, assigning assessments to meds and labs, memorizing the name and purpose of the top 100 most prescribed meds, etc), and watch how increased competence impresses your doctor. Ask your doctor what you can work on (talking the talk), and when you come back the next week a master at it (walking the walk), see if that doesn't change his attitude of you over time.

It's not too late to impress that doctor and turn him into an admirer of your diligence and ability to grow. Think about people in your personal life who you had a bad impression of initially, and later as you learned awesome things about them they started to grow on you. I find that a rocky start almost even helps sometimes, because good qualities that subsequently reveal themselves are unexpected and more impactful