well he is probably uncomfortable- Layla hates it and i've been doing it since she was a puppy.
I put Layla on her back and pull back her cheeks. Do you use an infant toothrbush? These are better because they are small and soft bristled. Otherwise- you just gotta do it. He will keep whining because he keeps winning (you stop brushing). I do it every morning and every morning she hates it.. lol.. but i'm getting faster and it really pays off. Layla's vet always comments on how nice her teeth are