All dogs are descended from their wild cousin, the wolf, and share many traits seen in wolves. Dogs, and puppies in particular, are denning creatures and feel more secure in small, snug areas with low roofs, thus the success of the training crate.
Dogs are pack animals and do not enjoy being alone. Puppies who stay with their litters until eight weeks old easily will become members of human packs/families. Each pack needs a leader. Ideally all human family members should be ahead of the dog in the pack order. Your dog should not be the leader, as this can result in aggression or other dominance displays.