What this quote means is that racism is part of the fabric of the society in Maycomb. The quote means to put two sort of different faces on this idea.
First, it is saying that there is a good side to Maycomb. It is saying that the missionary teas are an integral part of the society. Second, thought, it is saying that there is clearly a dark side to their society. This is the side that is willing to act in extremely racist ways. The quote that you mention is saying that both sides are equally a part of the society of Maycomb.
By saying this, Atticus is saying that the kids need to understand that both of these are parts of the society that they live in.
Just after Atticus says this, Aunt Alexandra responds, "You are the last person I thought would turn bitter over this."
This shows us that Atticus' quote is referring directly to hypocrisy.
The Missionary Tea in Chapter 24 is one of the most blatant portrayals of hypocrisy in the entire book. The "high society" ladies discuss the need for Jesus in all remote parts of the world (out of an assumed love and care for those less fortunate who have not had the opportunity to hear the truth). They speak as if they are good Christian women who have a heart of giving and serving for humankind, but then turn right around and badmouth Atticus and the proceedings of the Tom Robinson trial.
In context - the above quote is a reponse to Alexandra's desire to shelter the kids from reality in Maycomb by chastising Atticus for letting them listen to the trial. He appeals to her by attacking something she's not only familiar with - but something she supports - the Missionary Society. Atticus compares the racism and hypocrisy in the courtroom directly to the racism and hypocrisy of her tea's - and believes the kids need to experience both.
In Harper Lee's To Kill a Mockingbird, after Jem is so upset about the trial of Tom Robinson in Chapter 22, Atticus tells his sister, who objects to the children's having attended the trial, that the proceedings of that trial were just as much a part of Maycomb as are the missionary teas, which also are examples of prejudice towards the blacks. For, in the parlor of the Finch home, the blacks have been just as much tried and convicted unjustly as Tom Robinson has been. For instance, Mrs Merriweather maligns her maid Sophy as Tom is maligned unjustly. Calpurnia, the trusted and loved servant of the Finches, is no allowed to bake the little cakes for tea.
These incidences of social inequality are part of the culture of Maycomb, Alabama, as are the games that the children play, or the gossip of the old men outside the courthouse, or Miss Stephanie's gossiping voice.