I think you have to sort of start off slow, not over handle him too much when you first get him when he is still frightened. Give him some days or a week or so to settle in and just get used to you petting at the most, and moving things around like his food etc.
Most of the articles I read about getting a new rabbit said to just leave them alone without picking them up at all at least for the first 3 days. Mine was like that, and from a pet store as well. I have had her two weeks, and gradually she has just become more and more comfortable around me with being petted and held.
Also, are you holding him close to you and supporting him when you hold him? and perhaps getting down on the ground at his level is a good idea. You might seem less scary that way. Rabbits are apparently afraid of heights. I usually try to get down low and pick her up, hold her to my body and then rise. And I also get down on my knees when I release her again gently.
Also perhaps you try calling him and holding out a treat so that he comes to you and associates you with a good thing. And could give some food or a treat and then pick him up and still hold it. So that that way, he will associate being picked up with a good outcome and not too scary.