Hey there!
I know exactly what you're feeling, I've had a Netherland Dwarf for 1 week now (he's 8 weeks old) and in the beginning he would run from my hands when i put them in the cage to pet him or pick him up. He still does when i try to pick him up, but when i pet him he'll just lower his head and not move while i pet him instead of running which is nice.
I started putting him on my bed while i watch TV, he'll run around, dart/bounce around now and even climb up onto my chest and smell my face etc, thats when i pet him (in which case he'll lower his head and not move), but its better than when i used to try the same thing and he'll run to the other side of the bed and come nowhere near me!
So just keep handling your bunny, talk to it, play with it as much as you can! (Its still early days for both of us but i've made good progress in a week so just be patient!).