The natural selection that takes place does not happen in humans - it happens in the virus itself. When a patient has been vaccinated against the flu, they build up the antibodies to a particular strain of the flu virus.
Since the patient has these antibodies, the virus is unable to get into the patient's cells, and they cannot reproduce. However, if there is a mutation in the virus, or there is a strain that the patient has not been vaccinated against, they can then invade the patient's cells - allowing them to reproduce and cause illness in that patient.
So the virus that is unable to reproduce is then losing the 'natural selection' battle against either the mutated virus or a new strain that has become present.
