I have found personally most 'savvey' Vet's are reccomending Chlor Palm now over baytril.
I don't understand why they gave you pills and not a liquid?
Also, Ear infections usually have an inflamation of the inner ear... you should be able to see that.
And Ear infections are also a 'infection', and my thoughts right now are infections usually give the animals a fever, What was your bunnies temp?
As for the pills, they sure do sound like a nightmare.
You want to hold your bunny up, like holding a baby upwards in a sitting position. Put the syringe in the corner of the mouth, but past the teeth, and squirt bits in at a time. He should kind of start licking it back.
You may want to add a little flavor so he likes it better. When I was force feeding my one bunny I added some apple sauce to give it a yummy flavor, so some juice could work the same instead of water.
I would call a few more Vets, find out if they take bunnies, and how often the Dr's see's them, or ask Rabbit clubs/breeders in your area who they go to. And maybe get a second opinion, even if it's just over the phone.
I hope your little bun is feeling better soon! <hugs>