It's like with real genetics. All people can run, some better than others. But just because your father was a track star, doesn't mean you'll instantly be one. You still have to work hard to get that physique.
It's the same with your Charmander. Just because both Dragonite and Charmander learn Fire Punch and Thunderpunch via Move Tutor, doesn't mean Charmander can learn them by breeding. In fact, Charmander will never be able to have Fire Punch through breeding.
Just look at his Egg Moves. Those are the ONLY special moves able to be obtained.