I honestly don't think you are being over protective. Yorkies are very small and fragile and therefore, if a bigger dog was to snap at them it could be fatal. Better safe than sorry. If your puppy is friendly that is a good sign that it will not be hard for him to socialize with smaller dogs his size.
Maybe exposing him to dogs that would snap and bark at him will cause him to become less friendly in the future thus his social skills with other dogs will decline. I am thinking that early exposure to snappy dogs could also cause your puppy to become timid and nervous.
