3 causes of disease I can conceive:

1) Endogenous - the disease is somehow inside us all the time (eg genetic disorders)

2) Environmental - we are exposed to some sort of harmful condition (eg radiation, toxins, pathogens if any can be shown to exist)
For example, paralitic polio was probably caused by the pesticide lead arsenate.

3) Deficiency - we lack some element for ideal health (eg some vitamin/mineral, sunlight, fresh water, etc)

I suspect that in the case cold & flu illnesses the body is reacting to cold & diminished sunlight (and thus vitamin D conversion) during the winter months.

If flu is caused by a virus, why is it seasonal? Why does the virus care how sunny it is or whether it's 30C or 10C outside?