I've had very bonded ducks and ones that took along time to warm up to me. Ones that hatched here and I was able to bond with from day one are the most comfortable with me. It really helped that the mom tolerated and trusted me messing with her ducklings.
The two that I bought when they were three or four weeks old are just now letting us pet them and are finally eating from our hands. It was only after they reached the age of mating and laying that they began to really relax and not act as if they though we were axe murders. All ducklings tend to go through the frightened of anything bigger than they are stage. It really makes sense when you look at how a typical duck flock works. The ducklings get picked on horribly by all the adult ducks except their mother. Very sweet normally nice ducks can't seem to help themselves, they nip and chase off the ducklings as a matter of course. It's a pecking order thing. The ducklings have to be constantly wary, ready to sprint to safety anytime a larger duck gets close. If they let their gaurd down even for an instant, somebody takes a bill full of feathers out of them. The mother ducks is very agressive protecting brand new ducklings but after a few weeks gets pretty darn casual about it. It's a good thing ducklings are fast compared to the slower moving adults.
Mating hormones, the ones that drive a male to get all grabby feely with females and cause females to allow themselves to be grabbed, nuzzeled, climbed on, stomped, practically drowned, groomed and mated are often what finally causes a duck to calm down and accept human interaction again. Ducklings that lived in absolute terror of my drake are now closely following him, snuggling and napping with him. Those same ducks, one random day didn't flinch away from my hand and let me pet them. If they are scared of you, be around them without trying to touch them. Do interesting things like digging, messing around in the yard or even splashing your hand in the water dish. Offer treats and talk to them alot without much eye contact. Ignoring them makes you seem friendly and trust worthy. Odd, I know. If bigger ducks come at them, don't run toward the duckling, trying to scoop them up. Face away from them and chase off the adult.
If they are really young ducklings holding them on your lap can really help you bond. Don't hold them in a way they feel trapped, instead put your hand flat lightly against their head or tuck them under your chin. Hunch over them or make a towel cave. Try to mimic a mother duck, she doesn't hug or grab her ducklings, she might touch them breifly with her bill, but mostly just provides a soft sheltering ceiling of protection and warmth.
Sorry for rambling, and some of this doesn't apply to your situation. Don't give up, it will get better.
