With these words, Calpurnia is telling Scout that not everyone is the same -- however, just because someone is different doesn't mean they don't deserve kindness and respect.
She means that Walter Cunningham may be different (and have bad table manners) but that doesn't mean Scout should be mean to him. Walter deserves kindness and respect just as much as someone with good manners.
This lesson relates to the novel's larger themes of racism and equality. Black and poor people were looked at as "less than" white people. As a result, many people thought it was okay to look down upon them and treat them poorly. This lesson proves that it's never okay to treat anyone badly.
It's important this lesson comes from Calpurnia, who is an African-American woman. As such, she would know what it is like to be treated as "less than." She is letting Scout know it's never okay to think you are better than someone else.