My rabbit likes to be picked up and held, but he doesnt like to be taken out of his cage.. why?

I have a dwarf rabbit who is fairly new to us (2 or 3 months) He is very sweet and likes to be held, walked and pet, but when i try to get him out of his cage he refuses. i try to get him out with treats and even singing lol. but that didnt work. If i just reach in and grab him when he isnt looking then its fine but when he comes up to the door and i try to get him or pet him then he runs to the back of the hutch. At first we had a small wire cage and he was fine but didnt have much protection. So we got a bigger one with a shelf and lots of room (all walls are wood except for the bottom and from which are wire) what is wrong and how can i help it??