When I first took Rylie to puppy class there was a small puppy and two large ones. Rylie was terrified of the small pup and loved the two biggies (they were all about the same age) - I took him to a different puppy socialization class and he was afraid there as well. I just kept taking him places and praising him for calm behaviour. We went wherever I thought there would be dogs We did obedience this winter and my two were asked to stay and play with the puppies - this time Rylie did fine. There is no doubt that he's more comfortable around larger dogs, although he is able to enjoy himself now in the small dog section of the dog park. I think that's partly because nearly all of our training has been in classes with larger dogs.
I'd say just keep exposing him to situations (for small amounts of time) and don't react when he makes a fuss. Also get a harness he won't squirm out of. That could be really dangerous.
Mindy Tri - Feb/97
Max - Ruby - Sep/08
Rylie - B&T - June/09