Yeah - most bunnies hate being picked up - their instincts scream "OMG SOMETHING'S GONNA EAT ME!!!!". You just have to respect it. They can be taught to tolerate it, but most never like it.
I do really well with getting down on the floor with my bun, and letting her approach me. Being a bunny-jungle-gym is fun! But she won't even let me pet her except when she is sitting in a couple of designated "pet spots" - one is up on a bookshelf, and another on the futon. You just learn to adjust to their habits and quirks - that what makes them so fun!