As others have said, they get over it. Quickly. Treats help.
I've had to do many unpleasant things to many animals (cats, dogs, rabbits, sugar gliders, birds, even a turtle) for their own good over the years. Seriously, they get over it. Many of them seem to figure out afterward that the "icky" thing you did was actually for their own good. For example, getting flipped over and claws trimmed sucks to many rabbits but when they're upright and running around with appropriately short nails, they realize they're more comfortable that way. That doesn't mean they won't fight the nail trim just as hard next time, but it does mean they won't hold a grudge.
An example: one of our sugar gliders (who was wildly, angrily un-bonded with us at the time) was making weird noises and straining to poop a few years ago, so I took him to the vet. He got scoped and x-rayed and it turned out he had inflammation in his lower intestine. I had to syringe nasty-tasting antibiotics + metacam (pain med) to Mr. Bitey-pants once a day. Even with a feeding tip (cannula tip) on the syringe to help get his mouth open and make the droplet of meds smaller, it was quite traumatic to both Hobbes and myself to medicate him on the first day because he had zero trust for me. Day 2, I expected to be in for a major fight yet again... but when I pulled him (and his fleece pouch, which protected my hand from his teeth) out of the cage and approached with the syringe, I was in for a surprise! His mouth popped right open for it, lol. Clearly when I gave him the pain killers the first time, he started feeling better shortly after and connected the two experiences, making him quite receptive the second time around.
We've had 7 rabbits over the course of the last 7 years and "mommy" (ie me) is always the 'bad cop' in our house. I'm the one who has to do anything nasty that comes up with our animals - syringe medications, force-feed, trim nails, cut burrs out of the fur of a cat who escapes outdoors, clean up poopy butt, get eye boogies (rabbits appreciate that but cats LOATHE it), wipe snotty noses (our newest cat passed around a URI to the other four cats after we brought her home), you name it. If an animal doesn't want us doing something that needs to be done, then it's "mommy's job". Worst-case-scenario, an animal holds a grudge against me for about 5 minutes. I've made a mistake on rare occasions that caused minor pain - no one's perfect - but it really doesn't matter in the big scheme of things.
I can't stress this enough - do what's gotta be done, fork over a treat or two, give a nose rub and get on with life; your rabbit will do the same
.