Truthfully, most rabbits hate to be picked up/held. They're prey animals and relate it to being caught for food. My rabbit, Honey, will tolerate my holding him for about fifteen seconds before he struggles to get down, so I only pick him up if I'm bringing him outside or checking his nails/teeth.
And some rabbits dislike it more than others--I know one rabbit one of my co-workers has completely flips out when he thinks you're going to pick him up. If you want to get to know your rabbit, I suggest spending time on his level. Sit on the floor, let him come to you, pet him but don't try to force him to stay with you. Honey loves to sit there while I pet him--he'll sit next to me for twenty minutes, but has no interest in sitting in my lap, lol.
To get him to go in his cage, do you have a treat bag you could shake so when he hears the noise he comes running? Then he could relate going in his cage=treat and you wouldn't have to stress him out by picking him up and forcing him in, as his cage should feel like a safe place and not a place he's upset about.