Higher temperatures are not uncommon in children. You are following the best course of treatment by staying in contact with your physician. Your physician has seen your son and has reacted appropriately. I would continue what you are doing for now.
I am not a doctor. I do, however, read out cultures and am a medical microbiologist.
That being said, there are LOTS of really resistant bacteria out there that reside in middle ears. Children in day care are especially vulnerable because they're exposed to lots of kids.
My daughter, who is now 24 years old, went through at least 15 ear infections in her first five years of life. She had ear tubes put in three times and ended up with bilateral tympanoplasties to cover up the ear tube holes when she was ten years old. Back then the bacteria weren't nearly as resistant as they are now. Luckily, I never had to deal with what you are going through. One time, though, after her tube had fallen out, but the hole had not healed, she had a nasty infection. She woke up screaming from a nap. She was still in her crib, so was quite young. When I ran into the room, yellow green pus was streaming out her ear. Luckily, it burst out rather than in towards her spinal cord and fluid. I cultured it and it grew Group A beta strep, Hemophilus influenzae, and Streptococcus pneumoniae, all of these being respiratory pathogens.
I have been told by my Ph.D. microbiologist at our lab that there are strains of S. pneumoniae that are Zithromax resistant. I'm not sure what their incidence is in pediatric populations. S. pneumoniae is the most common bacterial pathogen of the CSF (spinal fluid) of this age group. It used to be H. influenzae, but your child has probably received the Hib vaccine so that is not as great of a concern as it used to be. This bug is still out there, however.
The dangers of protracted ear infections is that they can lead to bacterial meningitis. If you notice any swelling of your child's face or head, or extreme lethargy, headache, stiff neck, sensitivity to light, get him to the ER immediately.
http://www.emedicine.com/EMERG/topic390.htm
I am posting this URL not to scare you, but alert you to possible symptoms that your child's ear infection may have progressed into something far more serious. You can't have enough information. Believe me, I've been there.
I know that a lot of pediatric handbooks will tell you that kids can run high temps, yada yada, but as a micro person, I wouldn't mess around if your child keeps running these.
Have they done cultures from his ear? Blood? Throat? Spinal fluid? I know I've read about ENT docs making small incisions in ear drums and getting the pus out for culture, and thereby relieving the pressure, but I don't know how common that is done, as the patient must be anesthetized. I think the procedure is called a myringotomy.
http://tinyurl.com/445uk
You may need to have your doctor refer you to an ENT doc. My pediatricians finally threw in the towel. Of course, I wasn't dealing with an acute siutation like you are. You must be proactive.
As a P.S., my 24 year old daughter now has slight hearing loss. Not enough for a hearing aid, but I can see that happening down the road. Her most recent audiometry exam showed one ear worse than the other, as she has a piece of weird scar tissue on her ear drum from the patching surgery. I think it interferes somewhat with her eardrum function. Every doc that's ever looked into her ears after the surgeries takes a second look, as I guess the one is quite weird looking. She hasn't had an ear infection in at least ten years, however, so it finally does stop when their Eustachian tubes mature.
One thing I've read about that's highly implicated in chronic ear infections is the use of a pacifier. My daughter used hers ALL the time until she was nearly four. She threw it away herself, finally. If I had known then what I know now, I would have thrown it out when she was a young infant and put up with the screaming for a few days.
http://tinyurl.com/4smjm
http://www.drgreene.com/21_303.html
These sites are quite informative.
Good luck to you.