If the pup has had reoccurring problems with ear infections, that could be another reason he doesn't want to be cuddled. It hurts! People instinctively want to pet, pat, and cuddle a dog's head. If his ears hurt--and if he's tired of getting drops and people fussing with his painful ears--it makes sense that he isn't sure about getting close to people.
Petting on the chest and under the chin will help, but he'll have to learn that that's what people are going to do.
Cedar (tri), Willow (blen), & Holly (ruby)