But still, you get rabbits sometimes, that no matter what you do, they are shy little bunnies. Cinnamon was that way as a baby. I handled her more then all the rest, because I knew I was going to keep her from the start. But she was still really, really shy. Luckily she grew out of it around 3 months old. It also helped that even though she was shy and didn't want much attention, I still gave it to her. I rewarded her for behaving properly and letting me hold her, groom her, and give her health checks. Overcoming that shyness isn't only good for the bunny, but it's good for you, the owner, too. It's just not fun to have a bunny that won't let you clip his nails; pet him; give him cuddles and squeezes.
To become best friends with a bunny that's on the shy side, remember one thing: go at his pace. If he wants to stay at the back of the cage and be ignored, let him. He won't stay this way forever.
Once he is showing interest, try feeding oats or some other treat (if the bunny is over 6mos old), out of your hand. If he won't take it, put it in his dish. Try this daily. He will slowly realize that you are his friend; and that when you enter the cage, good things happen!
All rabbits love to be pet and loved. Some are just afraid of something that happened to them in the past. Rabbits are shy by nature. So if the breeder/previous owner of the rabbit didn't properly train the rabbit, they won't know how to not be shy. You will need to train them.