My holistic doctor thinks I had flu 3 years ago, wants me to take homeopathic influenzium 15c-5 pellets-1 x a week for 6 weeks.....Any reasoning?

Awkward. You should ask your doctor to explain his or her reasoning for this one. The way I use homeopathy is by matching the exact symptoms and experience of the patient, to what is known of the available homeopathic medicines. This doesn't seem to be what your doctor is doing, so i would suggest asking him or her for clarification.
No supporting data. The flu vaccine give you protection of the most prominent strains for that year, however not the only ones. Although it is not a promise of complete protection against other non-covered strains, the illness won't be as severe as without the vaccine. Do not confuse the flu (influenza) with a cold.