Hi Jamie,
Firstly, it’s good you’re are asking and willing to learn. I think your relationship with your rabbit can improve but just don’t expect the relationship to be like it would with a cat or dog or you’ll end up disappointed.
The important thing to understand is rabbits are a prey species. It basically means they are hard wired to think everything is out to get them. It’s what’s makes it so much more special when you do earn their trust.
I’m sorry, but the way you have handled him so far has proven to him he needs to be fearful. But you can change this!
Avoid picking him up. To interact with him, lay down on the floor and let him approach you in his own time. Even when he does come over, try not to touch him at first. After some time, you could start patting his head. He might even settle down and lie next to you for a bit.
When you need him to go to the cage, do use a treat as an incentive. I find with scared rabbits, that to put a box or carrier down they’ll hop in and I can take them back to the habitat that way. Sometimes I do need to herd them into the carrier but its still better then picking them up if they fight so much.
You can eventually work with them in being picked up but it takes time and patience. Most will tolerate it but rarely will like it.
I hope this has helped some and please ask if you have further questions. You’ve only had the rabbit a short time so I hope you’ll be able to enjoy things more and see all they can be.