Why do Water type moves hurt all Fire-type Pokemon?

Before you say this is a stupid question, let me explain. What I am asking is why water type moves hurt some fire Pokemon like Flareon and Vulpix. I can understand it hurting Pokemon like Ponyta and Magmar since their flames are on the outside of their body but it doesn't make sense that it also hurts Pokemon like Flareon whose fire is inside their body.