Chickens are jumpy animals, period. Think about it- they don't really have much of any defense against a predator other than to jump at him and squawk and fly (poorly) away. All of their predators are bigger than they are, so they all come from above them. Chicks are never, ever, ever going to NOT freak out when you reach down for them. It's in their DNA. Even my fully grown chickens, who are perfectly used to my family and me and are pretty trustful, don't like it when we reach down for them. We have better luck reaching for their breast area if we want to touch them.
They are chickens. They're not puppies or kittens who want your attention and petting. They're happier being chickens, particularly when you have a nice size flock like yours. I'm not saying don't hold them and handle them- you do need to be able to handle them from time to time. I had the best luck when mine were chicks by sitting down and letting them come to me and jump on me if they wanted. But generally, yes, they will be a bit jumpy.
