My nearly 4 year old daughter is was also very scared and wary of animals, especially dogs.
The local park is often frequented by people who let their untrained dogs run around off the lead – when she was about two, she was run at by a big boxer that was off of its lead. After that she was mega-scared of any dogs. My in-laws bought a rough collie pup about a year ago – my daughter was very wary of him to begin with. Now, even though he is quite big, she is not scared – unless she is surprised by him, or he is particularly boisterous. I would say she is just wary now.
My advice would be to let your son have regular contact with one well-trained dog (if you can) and let him build a relationship – maybe help with training if the dog is young.
If you can get him to the point where he is being wary rather than scared, I would leave it at that – being wary is not necessarily a bad thing for kids. My one year old son has no fear of anything at the moment – it sounds great, but I am worried he is going to be too confident and get into trouble!