It shouldn't be causing pain unless he already has problems going on (too young). You can just start slowly and have him get used to your finger first. I find that doing that type of things tends to be w waste of time with Ellie though. I have been brushing for 2.5 years and she has hated it for 2.5 years. She likes her toothpaste though.
I usually do it with her laying on her back. I hold her head with one hand and brush with the other. She tries to push my hand away with her paws and I just keep brushing.