Practically all rabbits hate being picked up. Most also heartily dislike being held. You know this already, but I do think all your bun needs is more time. It is of course important that he associates you with nice things like food and treats and for example unconditional headrubs.
A bun that has a bonded partner tends to be less demanding of human interaction.
It is difficult to train a bun to accept being handled. I do think the best thing is to slowly gain the bun’s trust with treats and love and by only very rarely picking it up. Buns that need to be handled a lot due to health problems will eventually become used to the procedure, but its very stressful for quite some time (often weeks) before the bun realises that putting up a fight is useless. You sometimes see people recommend frequent handling in order to make the bun accepting of being handled, but it may result in the exact opposite thing. With poorly buns we have to, of course, but that is a different situation and the rabbit has something to gain from it (medicine, wound care etc).