I was feeling the same way with my bun! He hated being picked up, would refuse his medicine completely and even would bite at me. I had so many bruises and bite marks all over my arm and some on my chest! 
But i persevered through the medicine, worried he would hate me at the end but i felt okay that he would at least be healthy and safe even if he hated me. Turns out, after a lot of doses of his antibiotics, he kinda got used to it. After i found the proper way to pick him up, he was easier to hold, he stopped biting, and he didn’t hate me after all.
In fact it kinda brought us closer i would think. I did things to help along the way. I would give him fruit after his medicine, or give him his veggies after medicine in the evening and then i would leave him alone for the rest of the night.
I wouldn’t pick him up without warning, i would offer my hand and pet him a few times before carefully and swiftly picking him up so he spent less time in the air. I would say things like “Good bunny!”, “Good Onyx!”, Good boy!”, in a really soft and calm voice. Even now, a week or two after his last medicine dosage, he still wants me to pet him and he even snuggles me.
Some bunnies, however, will never enjoy being held or picked up. But to help with the petting, don’t reach your hand in the cage. Bunnies are territorial and that’s their area, so they will tend to grunt and lunge.
Try to get him out of his cage, out in a pen, and just sit with him for a while before ointments and medicines. Offer your hand to him, and if he bows his head then give a little pet on the head once and take your hand away. This really helped with my bunny, who hated being touch or bothered at all at first. It showed him that if he didn’t want to be bothered, i would respect that and it got him to trust me more.
You can repeat this a couple times, as long as he doesn’t run away. If he does run away or just doesn’t bow his head, take your hand away and try again in about thirty seconds to a minute or whenever he comes back over to you. I was told to just sit on my bunnies level, and just play on my phone. Just to get him used to my presence.
Hope this wasn’t too long, and i hope it helped in some way!
