-지 않아요 is used for both action (오지 않아요) and state (크지 않아요). So, in questions, it means "Don't/Doesn't (subject) do..?" or "Isn't (subject)...?". 잖아(요)? is often used as a rhetorical question to make a statement, just as "Isn't that lovely?" in English often means "That is lovely.". Examples: 나는 아직 모르잖아요? == 나는 아직 몰라요. == I don't know (it) yet. 할 수 없잖아요? == 할 수 없어요. == Can't help it / Can't do anything. 너무 춥잖아요? == 너무 추워요. == It is too cold. When you are actually asking something, you usually say -지 않아요? When it's a rhetorical question stating something, -잖아요? is more common. And intonation of the sentence also determine the meaning. Your 아프잖아요? thus can mean "It hurts." (said flatly) or "Does it hurt?" (raised the end like a sentence).

It is basically a constructive way to negate something. You can use the adverbs 안 or 못 to negate something. In order for the above sentence to make sense, you can see the use of the negative form as a means of asking for confirmation. You could translate it to: it doesn't hurt, right? Which an English speaker would typically phrase as: are you okay? or does it hurt? The construction is often used as such. Any native speakers may of course correct me or add to my explanation!