I had this problem when I first adopted Theo – he wouldn’t tolerate being held at all. We did manage to train him to tolerate it – and now he will even lick our faces when we hold him.
We started by touching his belly for as long as he would tolerate and rewarding him with a treat. After he started to become okay with that we starting touching his belly and putting upward pressure on him as if we were going to lift him and rewarding him with a treat. We continued this positive reinforcement for the first couple of weeks. Then I would place a towel gently over his head to calm him and bunny burrito him before picking him up. This helped him be less stressed and feel more secure. We did this for another few weeks once a day, always rewarding him with a treat. After this we progressed to picking him straight up without the towel. For the first few times he would kick etc but always once he was up and secure we gave him a treat. We kept practicing with him everyday for I would say maybe 4 months and now a further 8 months down the line he actually likes being picked up. This has helped us a great deal as we have had to syringe feed him and give medication a few times in the past few months and this would have been impossible without the training we put in. It also helps the vet to get a good look at him and he tends to remain calm when the nurses handle him now.
I hope this helps and good luck! It’s a long process but worth it. Truth is, most rabbits will never enjoy being handled but most can learn to tolerate it for a short time- long enough to be examined by a vet or administered food/medication etc