I really think it’s a bit of both. Personality really comes into play, especially in the begining with a rabbit, figuring out their likes and dislikes. There are some bunnies that just will never tolerate really being held, and others who enjoy it, and plenty in the middle. I have over time been training Dutchess to being held more, since it’s something I really enjoy. When you pick up your bunny and hold him, make sure you support his back feet and his front feet and chest area, the more secure the bunny feels in your arms the more apt they are to enjoy it. I usually sit with her on a chair in the kitchen where she can’t jump down, and I lean and let her lay on my chest/torso keep one hand supporting her bum and back feet at all times. My other hand I pet her all over with, and because I’m partially reclined she isn’t in danger of falling. Dutchess has really come around to this a lot more, at first she would wiggle and hardly sit still, and now after two years I can cuddle with her for 10-15 minutes, and I stop and let her go rather than her wiggling to be free. She will close her eyes and purr quite frequently, despite the bunny foot flicks she tends to give me as she hops off when I set her down

My boys like to be held for about 10 min. at a time, but only resting on my lap!!! I usually will groom them and give them a treat. then I snuggle for a little bit longer. They will cuddle longer if they’ve been out running around for a while!!!

Honestly, some rabbits just hate being picked up and held. While others enjoy it. It all depends on you bun’s personality. If your bun is not too keen on being picked up it wouldn’t hurt to do some positive reinforcement after a holding session. It may help with the aversion. But it honestly comes down to your bun and his/her wants and likes.

http://www.youtube.com/watch?v=wyr3w8o145Q

Check out that video. I think the main thing is to make sure you support their feet at all times. Buster NEVER lets me pick him up. Literally, I can’t even touch under his belly because he bolts under my bed in half a second. But, when I do pick him up he cries and cries (once scratched up my neck like crazy), so he always gets a raisin (his favourite.) I usually try to make sure that he gets a raisin WHILE he’s being held. I read something that if you give it to them once they’re on the ground again then they’ll begin to only want to be on the ground so they get their treat.
Good luck

It’s important to be able to pick up your rabbit for transportation and management, but other than that I usually discourage picking up bunnies as they typically don’t enjoy it very much. You’re right that some rabbits don’t seem to mind it as much, and that this is largely a personality-dependent preference, but for those that dislike it, I wouldn’t force it.

BinkyBuster, does your bunny vocalize when you pick him up? Bunnies usually don’t vocalize unless they’re under extreme pain and/or fear; if being picked up stresses him out that much, maybe you could try spending more time on the floor cuddling with him instead of picking him up?

I only pick up my bunnies when necessary, like for grooming. Bindi will tolerate it for a few minutes but Olivia really hates it. I hold my bunnies against my chest with their head and front paws near my shoulder.

Peppypoo: yes, he does. He makes soft little squealing/crying noises. It breaks my heart so I only ever hold him for like a minute tops (trying to get him adjusted… not working too well.) The time he scratched up my neck I was SO determined to cut his nails. I told my boyfriend that I’d pick him up and he does the trimming. I got him, set him in my lap, and in the course of literally 2 seconds he FLIPPED out and scratched me so badly I had to let him go. I felt SO awful and again it broke my heart. Needless to say we take him to the vet for his nail trims… 

I do spend a lot of time with him on the floor, I just think because he was adopted from the humane society at a later age (3 1/2) that he likely didn’t get held much as a baby so never adjusted to it.