Sometimes dogs who are shy can be afraid of men. A reason is not always known. Maybe it's because men tend to be bigger and have deeper voices. Might be because the dogs can smell the testosterone
I suspect that for many rescue dogs, it might just be neophobia (fear of new things). A lot rescuers and fosterers are women. And some of these dogs probably didn't meet a lot of men during their crucial socialization period.
Regardless of the reason, pet guardians need to figure out a way to help the dog feel better about members of the household.
Note: The below is a guide. It's best to work with a professional. Especially if there is any chance of bites or injury.
And if there is no way to get the dog feeling safe, it might be best to consult a board certified vet behaviorist
Also note that the below info can apply to anyone whom the dog fears. Not just men.
Start with complete separation if possible. Split up the residence so the dog has no contact with the man or scary person. Then work with a trainer who can set up some controlled scenarios for success. Perhaps a neutral territory or outdoors with the scary person far enough away so that the dog is not concerned.
See some details here: http://www.stubbypuddin.com/2014/12/advanced-counter-conditioning-and.html
And here: http://www.stubbypuddin.com/2013/11/visitors-part-iii.html
Once back indoors together:
1. Scary person completely ignores the dog. No looking, no talking, no food from scary person. No feeding, no walks, etc..
A. watch how scary person enters room. Might need to come in sideways or backwards to help dog feel better.
2. Later, non scary person can treat the dog for presence of scary person. See counter conditioning and desensitization link above.
3. Later, non scary person can treat for scary person's movements.
Scary person lifts finger, non scary person treats
Scary person lifts hand, non scary person treats
Scary person lift arm, non scary person treats
This could take days, weeks or months.
Take your time.
4. If #3 goes well. Non scary person can drop treats as he/she walks by.
4a. Note during this time, the dog should not be encouraged to approach scary person at all. Teach the dog how to relax on a bed or behind a barrier that is a significant distance from the scary person. Reward the dog for keeping distance.
5. Later if dog decides to approach scary person, practice treat/retreat. Toss a treat away from scary so the dog gets a double reward. Food plus relief from pressure.
6. Much later, scary person can start rewarding approaches. i.e. scary person approaches from 10 feet away. Drops treat, leaves. The close the gap slowly (work with a professional)
Then when dog approaches, scary person can treat.
7. Later you can start rewarding touches. Only if touching is necessary. i.e. if the person is temporary or a guest, then touching and interacting is not necessary. If the person is going to be responsible for the dog (part owner), then touches will eventually be necessary.
Info on desensitizing touching here: http://www.stubbypuddin.com/2013/11/desensitizing-touching.html
Still no petting unless the dog is asking for petting. And then only really short, calm pets
Why food should not come from the scary person: http://www.stubbypuddin.com/2013/09/coaxing-with-flood.html