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The "N" word was a common term for black people. It was an accepted term used by the white community. Still it was offensive. Atticus was a progressive man and knew the common status quo was offensive, he wanted more from his children.
He's just trying to say that the 'n' word it not nice and that he doesn't want she to be listing to what other people say and wants her to like everyone even if they have different skin colour.
Because if Atticus told Scout the real reason why it was wrong to say "nigger" she wouldnt understand properly. But as he uses the word common she knows that it will mkake her seem a lower class and looked down upon in society. The word common is something that is looked ddown upon in scoierty thus suggesting that Atticus believes people that use this word are a lower class than him and he finds it offensive to use the word.