My nephew and his son have had horrible ear issues too so maybe it is something genetic that causes some kids to be more susceptible to infections.
I firmly believe there is a genetic component as well. I had lots of ear infections as a child and DD did too. It's an issue with fluid not draining from the ear because of the shape of the eustatian (spelling?) tube. It is more horizontal in young children which causes the fluid to stay in the ear. As the child grows, the tube becomes more vertical and the fluid will drain. The ENT I took DD to told me that the shape of the eustatian tube can be inherited and therefore issues with ear infections can run in families.
My DD had 5 ear infections in a 1 year time span. That was the threshold for her pediatrician to refer us to an ENT. It was a good thing he did. There was fluid behind her eardrums that wasn't EVER draining. It was enough that her eardrum wasn't functioning properly. The ENT described it as she would be hearing as though her head was under water.
She was delayed in speaking. I raised the issue at 15 months with her ped. He gave me the whole "kids develop at different rates, don't compare her to other kids" speech. At that point she'd had 3 infections in 6 months. In the next 3 months, she had two more infections which prompted the referral to an ENT. The ENT recommended the tubes, which we did about a week after our first appointment with the ENT. The doctor told us the fluid behind her ears had been there so long that it had the consistency of glue. Yuck!
The difference after the surgery was amazing. She's 4 1/2 now and hasn't had an ear infection since the tubes were put in. (They fell out a while ago.) And her speech took off around 2 weeks after the surgery! It was incredible how quickly she picked up new words after being able to hear properly.
As for preventing them, I know a friend who's doctor recommended starting decongestant anytime her child got a cold. It didn't prevent infections totally but she thought it might have headed off a couple. Other than that, I don't think there's much you can do. I also heard the connection between bottles and ear infections. DD was BF, but also got bottles so I can't speak to that.
I'd take your DS back to the pediatrician before flying next week to have the ears checked. If the infection hasn't cleared up, they can prescribe a different antibiotic. 2 reasons for this: 1) It's miserable to fly with an ear infection. My mom still talks about how they flew to FL when I was 2 and had an ear infection. Apparently, I screamed bloody murder the whole flight. The other passengers must have just LOVED that. 2) You don't want to be at WDW, far away from your pediatrician, and be stuck with a sick child who needs another round of antibiotics.
For soothing the hurt, warm, moist compresses on the ear can relieve some of the discomfort. Other than that, Motrin was my best friend when DD had hers. Nothing else worked quite as well at getting the fever down and making her comfortable.
Good luck!