bunnies, as a rule, aren't keen on being picked up, something to do with predators. i would sit on the floor with your bun and allow him to smell and jump all over you, it's all about getting him to trust you.
then you can try picking him up for a second and setting him back down.. building it up over time. some will get used to it but some will never, ever be comfortable and will kick and struggle within an inch of their lives! i've been lucky in that my bun isn't phased at all and will allow being picked up, it took time though...