How long ago did you take your son in to the doctor? I give my sons about 7-10 days then I take them to the ENT. I skip the pediatrician. They just pick up other germs from the doctor visit and I walk out with - it is viral!
Oldest had tubes at 3 mos., second has lots of diagnosed allergies. Both had their tonsils out as preschoolers. My older one rarely gets sick (7). Younger one is currently on antibiotics and will be (on and off) from Sept until April due to all those allergies. The other day, ENT said sinus infection and bulging eardrums - second set of tubes are out.
He is also on an antihistimine EVERY night and nasal spray. Zyrtec is great - he using something different due to problems with very difficult eczema.
I DO NOT like the antibiotics but know from the past that the younger one will not get better until he gets them. The older one would have a runny nose only then another visit to the doctor a day or two later he would have an infection. They will give you antibiotics for the ear infection but not the sinus infection (in my experience).
My younger son had NO runny nose until he was 9 mos old - this was the month of Sept, too.
I agree with the other responders that diet plays a large role in health. My son was allergic to a lot of the food that we were giving him and food passed along in breast milk but was not tested until he was about 18 mos old. Egg whites were a big problem for him. They are in baby foods. I would have sworn milk or wheat - but he is okay now with that.
Guess my point is - mom's intuition means a lot. Doctor's do not like to give antibiotics and that is great but sometimes your child needs them to move on and feel better. If all the natural suggestions do not work soon take him back to your doctor and be more assertive or try an ENT. Good luck!