D3 might help your immune system work properly, but it has no ability to protect you from the flu. If you are exposed to the virus and you do not have active (antibody mediated) immunity against it, chances are you will get sick. (Whether you get sick depends on whether you are exposed to an infectious dose, which is the minimum number of infectious particles that can make you sick.) In the case of influenza, I'm not sure that having a good strong immune response is desirable--strong immune responses are the cause of death for many influenza patients, as we saw happen to millions in the 1918 pandemic.
I take D3 because I have a lab verified D3 deficiency. I've had strep throat and two colds since I started taking D3 about 4 years ago. But in the 10 years before taking D3, I was sick maybe once. Therefore, the anecdotal evidence is that taking D3 makes me susceptible to infections. (Of course, that is not true; correlation is not causation.)