I'm not an expert on rabbits, but from everything I have read and my experiences I have learnt that it all takes time. Some bunnies will love to be picked up and nursed from the very second you get them because of how they were treated by their previous owners/breeder, whereas others will be scared and timid until they feel safe in their new home.
His behaviour sounds completely normal for a new rabbit. You haven't done anything wrong, but it just takes time to feel comfortable with a new person and a new place, and everything is very scary at first. It might take some time for him to not freak out when you pick him up, and this can be sped up a bit with giving him treats whenever he is held. Otherwise, just keep persisting. Wear gloves if his scratches are bad and don't let him back down until he is calm. That is then his reward, so he knows that if he is calm he can go back to his house if he wants to. Eventually, he won't mind because he knows you won't hurt him and he knows he is safe. It may take some time though depending on his personality.
You should also make sure he is confined to a small play area when out for the first few weeks and slowly increase that as he gets used to his new area. Everything new can be a threat and can scare them easily. His time out should also be limited and slow extended to make sure he doesn't become skiddish and scared. Try and lure him back to his cage with treats if you can so he doesn't associate going into his cage as punishment. He should go back to it frequently though if he feels a little timid of you.
Don't force it, but just be persistant. The more attention you give and the more he is picked up and nursed, the faster he will get used to it and the more he can get to know you. Just be sure to give him his space once he is good and calm and can be put down. Still be hear him and talk to him so he can learn you are not a threat, but don't try and overwhelm him with attention. This can make things worse.
Hope this helps!
T
