Hi Regza. You might have begun your post with:
I was in the company of a person a while ago and for some reason I got the feeling that she was looking down on me in some way. I have never got that from her before and there was nothing that she said or did to suggest that I was right but my gut is screaming at me! How do I know if this is just my own insecurities?
This feeling of 'being looked down upon' by a friend is a paranoia I well know. It may be less a question of empath/projection than a question of respect. You FEEL and feelings (intuitions) are your compass. The spirit revolts in the company of materialists and we are reminded too often of our anarchist strife to be who we are within and without, apart from the opinions of others. Because we walk a lonely road we are tempted to blame ourselves - which can pose for empathy. We are empathic because we ever look for a bird of our feather. That's the way empathy works. It is bilateral sense of 'you are I' and 'I am you'.

I think you have a very valid point. Empathy is always in part, projection.