Though I do prefer letting a bunny come out when they are ready, it has been three weeks and you are right, she could use the exercise, and as others have mentioned, she may not know how to really get out on her own. Is her entry and exit pathways pretty easy? How steep is the ladder?
I had this issue with my bunny Jack when we moved. He was never comfortable with change and it took him a couple of weeks to just explore out of his pen, and then after two more weeks of not exploring the rest of the house, I carried him to the living room to show him what he was missing. At first, he was a very worried bunny, but he soon became relaxed and after that, he didn't hesitate to come out and explore. Our situation may be a bit different because I had Jack for a few years before we moved and though he was not fond of me picking him up, he was used to me and knew I was not a threat.
I actually had documented his scaredy-bunny ways with photos back then (he has passed since).
Jack (white bunny) stayed in this pen and would not venture out with his bonded buddy Rucy. She would sometimes hang out by the pen entrance as if to say, "C'mon!, Let go explore".
This is about as far as he'd get...sometimes he'd just stay there and snooze.
He did eventually venture out to the rest of the bunny room but he couldn't get past the door - even when I put fun toys and tubes to explore that led out tot he hallway. He'd just hide behind Rucy at the door and then just watch her go explore the house.
So after 4 weeks, I broke my own rules of letting him explore on his own, and picked him up and took him out to the rest of the house. As you can see, he has a very expressive face -- he's very worried!
And once he got over his fear of the pillow, he relaxed and explored and ended hanging out like a King in the hallway.
Again, I usually encourage allowing the bunny to come out and explore, and come visit you, but usually this is when someone just got their bunny and they want this interaction to happen within a few hours or days. But you have been patient and it has been now three weeks. I would suggest though that if you do take her out, that you put her near her cage and ladder. You could also give her a little hidey box nearby on the floor so she has a place to hide for a bit and let her come out from there. (unless she ends up staying in there for hours!). Have treats ready!