No, fruit flies don't carry any pathogens harmful to humans. When I was younger we used to make our own vinegar with the help of fruit flies. When we were making wine we'd set some open bottles off to the side. The fruit fly would enter and lay her eggs. While she was doing that, she'd inadvertently inoculate the wine with the acetic acid producing bacteria. They have a symbiotic relationship. The acidification would be repugnant to fruit fly predators. Soon, you'd see the little "Vinegar eels" swimming in the wine. It wasn't long after that and you had Vinegar. Leave out a bottle of finished wine and they'll turn it to vinegar the first chance they get. Now you can buy, "Mother of Vinegar" to pour into the wine or fruit juice to make vinegar. More than the air born pollutant, the vintner puts air traps or "bubblers" over his wine fermenting finishing bottles to keep out fruit flies. Fruit flies aren't dangerous to humans but, they can sure ruin a good bottle of wine. The maggots don't present any danger to humans.
I make a bottle or two of wine every year. They sell Camden tablets to kill the bacteria and halt the growth of the acetic acid transformation. However, it doesn't eliminate the acid already formed.in the finished wine.