A. The fact that he doesn't seem bothered at other times is probably a good sign that there is nothing medically wrong that is causing this new problem...
It may just be a behavioral issue though, and not really because he has 'noticed his penis.'
In addition to stranger anxiety and separation anxiety, many older infants and toddlers develop a fear of taking baths.
Whether or not it is a new fear, it may help to distract your child when you begin the bath, like with some new bath toys or a washcloth puppet. Making sure that the bath water isn't too hot or too cold and using a mild bath soap might also be helpful.
It may also help to use a washcloth to cover your child's penis or maybe even let him take a bath in a 'swimmer' type diaper for a few days.
If those tips don't work, you could try to take a bath with your child or switch to sponge baths for a few weeks.