You just have to be brave and firm about it. You need to let them know they can hop away if they wriggle too much and get frightened by you holding them, because you don't want them being scared of you. I'm always very relaxed and forward when I rescue a new rabbit, especially one that isn't used to being handled. At the moment, my newest buck, a NZ white, is absolutely petrified of being picked up - he goes completely stiff and he pants heavily, then kicks/wriggles vigorously. That's totally different to how he is not being handled and I'm just near him, where he'll come and investigate me when I stand by his hutch, lounge about or come and see me when I'm sat in the run with him. Actually another 2 of mine are like that, really curious and relaxed when I'm near them, but they panic when I need to pick them up. Buster and Whisky don't like being handled, but they're at the 'tolerating it' stage now, and will, eventually, sit still when I need to catch them - for that I just crouch to their level (don't tower over them as that can be quite threatening - remember you're a predator to them) and offer my hand like you do a dog you first meet, let them sniff my skin or offer some sort of treat, and then try to touch their nose gently. If they let me, I'll rub their head a little, but it's totally up to them if they want to hop away, which they usually do. I eventually get them into a corner or at the side, all completely free again if they want to get away from me, and then they do lower their head in submission and let me pick them up, where I just flatten a firm hand across their head and back to stroke them, and with that hand I keep it on them and push it under their chest/belly, and as I lift their front up a little, I cup their bottom and lift them to my chest to secure them. Another of mine, Jake, he's a nosy little guy so will come over to me all the time, and though he hates being handled too, being picked up, he's really good at and will lower his head everytime I stroke it. Then there is Winston who has the run of my bedroom so he's extremely comfortable with being stroked and picked up, but again, like has been said, even the friendliest and cuddliest won't 'like' being handled - they do simply tolerate it.
You must stick at it though because one day you may need to help them medically, like hand-feeding them or giving them medication, and obviously with claw clipping it's dangerous to sort claws out with a wriggly pet.