Oooh, this sounds all too familiar!!!
Don’t worry, he and you will be ok, unless you keep thinking negative thoughts and get annoyed with him. They pick up on our feelings and won’t go anywhere close to us. It’s kind of like when a horse throws you off his back because he can feel we are scared of being up there.
We have two rescued bunnies here, both came from a shelter environment. Velvet was on deathrow because she was so aggressive. When we decided to foster her, I thought, ok, a shy bunny, I will just leave her alone so she can chill over here. Wrong. She was so scared that she was going mental. She would attack everybody and everything – except for my husband! I knew she did not like me in the least bit, I knew she must have been traumatized by women somehow. So I stepped back and let him be the one petting her and loving her while I would just sit in front of her x pen, talking to her and telling her I understood her pain and still loved her. I would tell her over and over again how pretty she was and that she was ok here. When the rescue lady met her again after a few weeks, she could not believe this was the same rabbit. Velvet now is a complete butterball! She looooooves people, she loooooves bunnies, she looooves life – she loves everything and everyone. There is not a mean bone in her body. She will flop over to the side for me to pet her. She is so very loving towards everyone, it is very heartwarming to see! Of course, I know daddy is still number one in her life, but that’s ok with me.
Dancer is extremely shy. When he was taken out from the shelter, he would do nothing else but hide underneath a box in his x pen. The slightest noise or movement and you wouldn’t see him anymore for hours. Only last week have I seen him relax and stretch out in the middle of the x pen, his legs to the side, his big bottom in the air, absolutely relaxed! I won his love over with healthy treats. He knows when he comes up to me, no matter whether I am standing or sitting or laying on the floor with them, I won’t pick him up (he greatly dislikes being picked up), I won’t tease him, but I will give him scritches and a treat. He even comes up to me just to get a facial massage now. It did take him a good two months though to get to this point.
As everyone else said, patience and understanding will help ‘Ninja’ to get over his fear and trust issues. It may take weeks, it may take months. As long as you accept him for who he is, he will come around and accept you in his life, too.