Woo, sorry, wall of text ahead- I'm a psychology major, so...
Rabbits naturally hate being picked up, but then, cats naturally hate being bathed- you can do both to either with proper conditioning... theoretically. There are always some individuals that just will not be shaped no matter what you try, but persistence tends to pay off in any animal.
I treat training for all species of animals exactly the same- reward for good behavior, prevent bad behavior, redirect if bad behavior happens, and be mindful of associations they might be forming all on their own. So this formula, for teaching rabbits to be okay with being picked up, would probably be like...
Pick them up even when there is no reason to, and often times, to bring them to good things. If you only ever pick them up when it's something unpleasant to do, like nail trimming, they'll see it as a Very Bad Thing. It's kind of like how dogs who only go in the car to go to the vet will probably be nervous and carsick every time they're in the car. I started picking up my rabbit to bring him to a bowl of his favorite foods, for example. Once he got more relaxed about being held, I started giving him a treat while I was holding him (but before that, he was too busy struggling to take a treat while being held).
To prevent the bad behavior (struggling), you have to be very firm and not give them any opportunity to run, or they'll be rewardind themselves by getting away from you every time they get out of your grasp. I tend to, while down on my knees next to him, scruff him first, then secure the back legs, then very quickly bring him in against me. Keep the back feet supported so that he doesn't kick. Usually, once Magellan is in against me, he relaxes slightly- though he won't be enjoying himself. I think at most all we can do is teach them to tolerate it, not like it.
I understand the mentality of not wanting to pick them up anymore than necessary, but in the end, I think this only causes the rabbit more stress when you do have to pick them up. It's inevitable that you'll have to at some point, so you might as well get them used to it so it's less traumatizing when it has to be done.
That said, I only have one rabbit. I'm just speaking from my experience in dealing with him and other animals using this same basic idea. I've never had it completely fail when it came to changing any behavior.
Also, as others added here, do it on the ground! You don't want your rabbit to fall. Plus, starting off by just holding them on the ground and gradually working up to holding them while standing is a sort of building up thing. It's much more gradual than suddenly grabbing them off the ground and up to human height.