Rabbits happily letting you hold them is actually not the norm, even here. Most of us don't hold our rabbits except when necessary, because they just don't like it. Rarely do rabbits like to be held, they're ground dwellers. They like those little thumpers firmly planted on the ground or solid surface, not hoisted up into a predators arms. Which is essentially what we are. There is always going to be the rare exception. I've had a rabbit or two
out of dozens, that have liked me to snuggle them. The rest get extremely offended and upset when I have to do it even minimally for health checks.
And some of those people that are able to hold their rabbits, have spent months or even years, building that trust to be able to do that. So yes, patience, and lots of it. That's just the kind of pet rabbits are. Ones that require us to patiently earn their trust. But it's so worth it when you see the results and you see it happen.
One thing I would suggest if they're reacting to sudden noises, is to get them used to background noise like music. You can even keep it going all of the time(not too loud though). This can help them learn to tune out noise so when unexpected sounds happen, it's not such a loud and sudden thing to them. Also movement. Sudden movements could be startling your rabbits. You might need to slow down your movements and make things more gradual if you are noticing this being an issue.
We are used to our environment and the way we move and the sounds in our environment. Think of it from a rabbits perspective in the wild. Loud sounds and sudden movements usually mean a predator and danger, and that they need to run and hide.
Nudging you with their noses is really good. It's them showing you they trust you enough to engage in interaction. But unless they're putting their heads down and asking you to pet them, forcing petting before they're ready and want it, is kind of like offending them or going against the proper grooming hierarchy in rabbit body language. Right now they're trying to establish that relationship and hierarchy with you. But because they don't speak human body language and you don't speak rabbit body language, there is this block between you in communication and how to progress to build this trusting relationship and understand yours and their place in the hierarchy. Rabbits are a herd animal, so relationships are all about hierarchy. And there is a proper way to do things in their way of thinking.
Right now, I would hold off on any petting. It's clearly making them uncomfortable and they aren't ready for that part of the relationship. If you want to interact with them use their body language as a guide. Right now they're nose bumping you to get your attention. So try the same in return. When they come up to you, offer your fist to 'nose bump' with them. When they get to the point where they do want head rubs, when you 'nose bump' your hand with them, they will either lower their head to let you know they want head rubs, or may hold their head there waiting for it. Then you can try a gentle finger scritch and if the bun stays there or lowers the head, then you know head rubs are being allowed and asked for.
I think I also should talk about what it is that's meant by 'petting'. I don't know what you do or what you mean when you say you pet them, so I'll go into detail of what 'petting' and grooming means to rabbits. If it's just light head scritching on the forehead that you do, that's perfect, when the time is right and they're ready. But if the 'petting' is more than that, this could be part of your problem with them and would be why they are running away and thumping. Because more than gentle head rubs, especially at this stage, is you invading their bubble, their protected body space, in rabbit talk. Which can be a violation of trust and very upsetting to a rabbit.
Head rubs on the forehead is the rabbits preferred place for mutual grooming, which is what we are doing when we 'pet' a rabbit. When rabbits groom each other, it is most often on the face, around the forehead, eyes, and ears. Some rabbits can be sensitive with their ears, so you don't want to mess with ears at all in the beginning. Some rabbits don't like their cheeks or under their chins touched, so you don't want to go there yet either. And petting the body is very invasive and shouldn't be progressed to trying until you have established a trusting relationship with your rabbit and know what they like and will accept.
The reason full body petting usually is a bad thing and can upset a rabbit, is because in a rabbit colony another rabbit touching the back or hind end of each other is usually either for dominance displays, mating, or to attack. So if you are going for full body petting, this can be seen by your rabbits as you being either presumptuous enough to try and exert dominance/mating behavior, or that you are trying to attack them. And all of those behaviors are going to either be upsetting, offending, or scary to your rabbits.
So when the time is right, stick with a gentle head ''scritch' until you have built up a more trusting bond, then you can try more of a head massage to try and include the ears and cheeks. When you've built that trust, when you understand your rabbits better, then you will know what they like and what they are comfortable with in their relationship with you.
Here's another site to look at on rabbit body language, if you haven't seen it already.
http://language.rabbitspeak.com/
. I have handled them from when they were young, although the mail was about 3months old when I got him. 
