I thought it might be useful to share my experiences of having a adopted a dog who came with several fears. Many dogs seem to have come from puppy farms or other environments where socialisation may have suffered so this seems to be a common issue. Also it seems some pups are very sensitive and one incident at a crucial time can lead to fears developing.
In the early days, Muffin, was scared of many things both in the home and outside. Some of her fears we didn't really understand such as other dogs because she would at times actually seek out a dog that worried her and bark at it instead of avoiding it. With a lot of advice and help, we started to use counter conditioning techniques around scary things so we would give her treats if she saw something which scared her. The idea being that they will start to associate the scary thing with good things happening. High value treats work best. As this became second nature, we started to see big changes. Generally speaking, she is rarely upset when in the house. She is also okay with most traffic, horses, cows and bikes.
We still work on other dogs, noisy vehicles such as motor bikes, and traffic on a wet or dark night. We found it helpful to avoid the scary things if possible but deal with them if confronted, We cannot avoid traffic completely as we have to walk a short way along the road to get off road. Also we have learned to weigh her mood up. At times she can be a bit more anxious and we will avoid any triggers if possible. Other days she seems more relaxed and does well. Yesterday she met several dogs without a reaction.
I think we will always have some fear issues but with time and understanding they are extremely manageable and impact very little on everyday life.