Most anyone who has raised chickens will tell you that around three weeks old their chicks seemed to get very scared of them. This can sometimes carry over to adult hood, and just makes taking care of them much harder (and a lot less fun!). There are some relatively easy ways to earn their trust back. Main thing you will need to do is nothing! Just go into their coop and sit there, don't talk or move, just sit. This will allow the chickens to come over to you without them feeling like your going to jump out and eat them! their curiosity will get the better of them and they will peck you, and maybe even jump on you. Do this for a few days, then bring food with you. The chickens should be getting accustomed to you by then, so when they come over to peck and explore you, hold out your hand and show them the food. They will eat it up very greedily and look for more.
Chickens actually learn very fast, and will very quickly start coming up to you when you walk into the pen. While feeding them pick one up, it is very important that you do this calmly. The chicken will struggle to get away, just hold them close. Begin to pet them with one hand and feed them with the other. They should enjoy this and will begin to let you pick them up with out struggle. It is very important that you are at eye level with the chickens when you pick the up! Otherwise they may think you are a hawk, and this technique will not work very well.
P.S. Every chicken is different so this may not work, this is just a guide line for you to follow. GOOD LUCK!