The House Rabbit Society manual has an entry on befriending the unfriendly/shy/timid bunny. You might want to read that section.

Essentially they believe that most, not all, buns can be socialized to interact with humans. It just takes a lot of time and patience!!!! The key, they say, is having the bun get used to you is by spending YOUR time with them down on the floor, at their level. Since buns are a prey animal they are inherently afraid of things that loom over them. When you are on the floor with them they feel safer, esp if you just sit there and don't talk or reach for them (L lay down on my stomach)....eventually their curiousity gets the better of them and they will come over to check you out. My experience is that some buns are very curious and will investigate immediately while others are so shy it takes them a very long time to get up the confidence to do so.

Do not give up and don't get discouraged. The key is to keep on trying.

I have one bun now 2 yrs old and he is just now letting me give him a bunny massage. Most of this delay is my fault as I didn't spend enough time holding and petting him when he first came. I try to spend an hour every night just sitting with the buns....I don't watch much TV but I do read and talk to them the whole time. When he continued to act like I beat him and abused him daily,I did what I suppose is a no-no....I forced myself on him...I would pick him up (when I could catch him)then sit on the floor and talk to him in a low, gentle voice and pet him and tell him how handsome he is.... it's taken a couple of months but he is finally approaching me. He will still run off if I move around too much but I think I've made good progress with him and eventually I am hoping he gets completely over his shyness.

So my advice is to try, try and try again. Good luck!