Some rabbits do warm up over time, others, well, not in the ways one would expect.
My late Red never liked to be touched, something that fully manifested during puberty, but she was a docile, friendly, laid back girl, got along well with other rabbits, including rabid dominant ones. But me touching her - no way.
When she got old and I had to brush, bath and medicate her she got somewhat lenient about that - still didn't like it and still tried to rip me to pieces when I picked her up, but - and that wasthe big change - she wasn't angry at me anymore

. No more thumping or so, no hopping away asap. Had a special, thick winter jacket for handling her, it now looks like I had several run-ins with Freddy Krueger

.
I think petting a shy rabbit works better for me when I keep the hand low and don't reach over them, just touch their side, shoulder that's facing me, like with dogs, and don't follow when it hopps away.