Give it time. It probably feels like an issue now, but it will most likely resolve itself as the pup grows, gets used to his new life, matures, and is trained.
I would definitely do handfeeding. When he gets his rabies shot (16 weeks, right?) I would think about a puppy class to solidify bonding and bud some confidence in him. He sounds like Duncan (though Duncan was a rambunctious little pup at times) in that he seems more mellow. Duncan my little sweet pup took months to really click with me and at a year old is still working on confidence. Agility, flyball, and all of the training we do at home have done wonders for him.
I hadn't thought of the confidence issue before because we also got him after having another breed - Papillons. Pierre is nothing sort of outgoing and brimming with self confidence. It didn't cross my mind until much later.