I think that it depends on the dog, how often that you need to clean their ears. If your dog was one of the wiggly breeds and would not hold still for you to clean its ears, then the vet would have probably been concerned about having you clean his ears. We used to have a big Collie when I was a child, and I don't ever remember my mother having to clean Bonzo's ears; so probably some dogs need it more than other dogs do.
If a dog seems to be shaking its head a lot, or having problems with its ears; then I think it is a good idea to clean the ears. I have used peroxide to clean my dog's ears before, and it seems to work really well.