Have you ever wondered why your dog, the one you've raised from puppy hood, the one who has never been abused seems afraid of men sometimes? Me, too. But, I have a theory.
When dogs are puppies, they are people magnets. People coo and shriek and cuddle them, but most of the people that find puppies irresistible are female. Girls, women or little kids all greet them with warm tummy rubs and high voices. Men, for the most part will give them a pat or ask a few questions of the human, but not give the barrage of affection they get from females. This continues into the dog's adult years so that the puppy makes this association.
Men can also usually be taller, have deeper voices and put off more of a dominant energy. Men also tend to wear hats more, which the dog often thinks of as something that doesn't belong.
This is another of the reasons that if you have a puppy, you need to get it out there in the world. Get him with other dogs, other people, other places anything you can think of to make him comfortable with everyone and everything.