At the Humane Society I help at, we get a lot of "badly behaved" rabbits. They bite, they scratch, they don't let you pick them up. We find that with a lot of them, they have learned to hurt people because it gave them what they wanted. For instance, if they didn't want to be held, a bite to the human made them put the rabbit down. We solve this by NOT giving the rabbit what they want when they bite you. If a rabbit we're holding bites, we don't put it down immediately--we grin and bear the pain, and put them down later.
Of course, sometimes when you're bit (especially if it's hard) the reflex to move away is immediate. In those cases, we try to determine whether it's a general aggression issue, a hormonal issue, or a cage territorial aggression issue. Many of our bunnies are only aggressive in their cages--when they're on the floor for run time they're fine. Neutering/spaying helps, but some bunnies will just be protective of their space.
The way I deal with this is to gradually and slowly impinge upon their space until they decide they can let me in. My bf's rabbit Frida is like this. She is free-range, but we had a small pet tent from Ikea that was "hers". If you put your hands anywhere near it, she'd lunge, growl, box, and bite at them. I fought the urge to pull away at hearing her growls, and took a few beatings, but kept my hand in the tent, petting her on the ears the way she likes. Now, she will still lunge at my hand, but not bite it. It's progress to me.
The shelter bunnies that are cage aggressive, I try to pet them in their cages, and let them get comfortable with me during floor time--climbing on me so that they know I'm not going to hurt them. We try to put them on the bottom level of cages so that our volunteers don't have to reach in there to pick them up to take them out for floor time--they can just jump out. We sit on the floor with them during play time and either ignore them or gently pet only when they come up to us, so that they know we're nice. I've seen some bunnies that were very scared, shy, and aggressive really turn the corner and become sweeter bunnies. A lot of times the aggression comes only from fear.
edit: I wanted to add that we have one that bit and held on for quite a while to me--I still have a scar from that! He's getting much better but you have to be really careful with him. Bored bunnies are also aggressive, it seems. Giving them something to do really helps.
