Taking anti-biotics doesn't help Upper Respiration Infection.
Anti-biotics only helps fighting bacteria infection but not virus infection.
For some tougher virus, the fever can lasts for 5 days.
If the fever doesn't stop, that means there're still virus inside the body. It can be Media Otitis sometimes. It's wiser to see the doctor again.
As for the fever, I thought we can take the fever medicine every 4 hours (i.e. max 6 times a day if necessary). You can also let your son bathe in warm water for about 15 mins to lower the temperature.
Hope it helps and hope your son will recover soon.