Based on context clues, I've always interpreted nose-bonks as a sign of affection. Rabbits are like cats. They're independent and like things on their terms. It's often hard to tell the difference between indifference and love, lol. The difference between them loving you and finding you annoying, however, is frequently expressed with a nip on the bum!
My husband and I have had 7 rabbits over the years and I've managed to turn every single one of them into a cuddle-bunn. Here's my advice if you want to teach a rabbit to enjoy cuddling with you:
~ Don't wait for him to come to you, because he'll happily do his own thing indefinitely. If you want cuddles, scoop him up and take him to the cuddle area.
~ Lay down with him. The vast majority of rabbits do NOT enjoy being held in your arms or your lap for cuddles - like JenGibs said, rabbits like their feet on the floor (or mattress/sofa). When I want snuggles, I take a rabbit to our bed and lounge in front of the TV with them.
~ Hold the rabbit firmly. Not "Elmyra" firmly (for you "Tiny Toons" fans
), obviously, but snuggle the bunny tightly enough that they feel secure (and as JenGibs said, 'wrapped up'). Let their little body get pressed up against your chest where they can feel your heartbeat.
Now that our rabbits are accustomed to being snuggled, I can move my arm (the one wrapped around them) away after a few minutes so that they're free to leave and they nearly always stay anyway.
~ Woo them: talk softly and pet their favorite spots - bridge of nose, ears (and the super soft part right behind/between the ears), cheeks, etc. Give the occasional treat or hand-fed pellet.
~ Speak their language once in a while. I periodically 'chin' our rabbits, especially when trying to strengthen a bond. They know darn well exactly what it means if you gently rub the bottom of your chin over them. In rabbit speak, it means "I like you. You belong to me now."
All four of our rabbits are happy for a chance to snuggle up with 'mommy' and watch some TV. Layne (RIP) used to lick the heck out of my pillow for some reason. Alice always 'grooms' me by licking my arm. Barnaby closes his eyes and melts into my arms. Nala loves it sometimes; other times she wants to run around the bed... but when I let her have her way, she always periodically comes back and nose-bonks me to say "what's up, mom?" Harley Quinn was the most resistant to the cuddling concept and it took a while (and a bit of pain from the times she decided to furiously 'dig' at my arm) to convince her that snuggles were fun, but now she gives up the love with the best of 'em.
Basically, if you want the cuddles bad enough, make 'em do it your way! The rest of the time (ie most of the time), respect their fuzzy independent streak and let them do what they want (which is often to use you as a jungle gym). To this day, our rabbits won't actually *ask* for snuggles, yet they seem to greatly appreciate being cuddled most of the time. I would say I let them do what they want like 90% of the time and maybe 10% of the time, I initiate a snuggle session.