We have them in a big pen in the garage until they can go outside.
And is that one with the tuff going to be crested?
I completely agree with the above suggestions about getting on their level. It is their natural instinct to be scared of things above them, like people standing above them and hands reaching down towards them.
I would also suggest letting them hear you before they see you. Whenever I went into the room I had my ducks brooding in I would first say hello or good morning. That would let them know I was there before I opened the door and they wouldn't be surprised by my entrance. After a while I would get happy chirps in response and they would be waiting.
Another thing I did was use bath time as a time to bond. While they were swimming around I would have my hand at water level or just below. When they were tiny and in the sink I stood up but when they graduated to the tub I would sit on the floor next to them. I moved my hand as little as possible and always slowly. Sometimes I had fairy moss, it's a floating water plant, and would give them handfuls. They really loved it and the only time they got it was at bath time. They eventually got used to my hand. They would eat from it and when all the treats were gone they would start climbing up on my hand and arm. One of them would climb on and then jump off into the water. Sometimes they would sit for a bit to rest. I talked to them softly the entire time. It really helped them learn to trust me.
And yes, looks like you've got a little crested baby.
You have received good advice. I would like to add that if they feel cornered, that makes it worse. Now, sometimes, that's unavoidable - but remember that when you work around them. I feel it's their survival instincts kicking in. They are small and vulnerable and it seems that at around 3 weeks of age, they suddenly realize it.
There is so much good advice here! I only wanted to add this: I whistle a short tune before even going to their area (first in the garage, and later in their outdoor place). After many days, they came to recognize this tune, and associate it with being fed, since i always brought food and a water change when whistling. And then whenever I brought peas (good old frozen peas, defrosted), I would whistle the tune first. BTW, peas are truly crack for ducks! It is not an exaggeration.
I am in the minority here, but I do not believe that ducks are here for us humans to pet, hold, and put in our laps. Sorry, that is my belief. I am perfectly satisfied that my little babies will come when I whistle or call, and stay about 4-feet away from me. It is not a breach of loyalty; it is not a lack of love on their part. I feel that if you need to pet something, get a cat.
I also have little songs and sayings I use around the ducks. One simple one is, "duck, duck, duck." And I start before I come into sight.