Another possible reason Calpurnia fusses over the children is that, in Atticus's absence, both Jem and Scout represent the face of the Finch family. The First Purchase Church is also geared towards an African American congregation and is not the usual place of worship for the Finches. So, Calpurnia wants the children to make a good impression; in her eyes, looking one's best in church is respectful conduct towards God and the congregation.
With Tom Robinson's trial in the community consciousness, Calpurnia may have also wanted to make as few waves as possible upon the children's entrance into church. Despite her efforts, however, she is accosted by Lula, a member of her congregation. Lula is upset that Calpurnia has brought Jem and Scout to Sunday service. She contemptuously questions Calpurnia's wisdom, but the rest of the congregation are supportive of Calpurnia. Zeebo particularly makes an effort to welcome Scout and Jem, assuring them that Lula is just "a troublemaker from way back, got fancy ideas an’ haughty ways..."
Most of the congregation are appreciative of Atticus's effort to represent Tom Robinson; however, members like Lula are suspicious of Atticus's intentions. In Lula's mind, Calpurnia still works for a white man.
Because of the Jim Crow laws, some African Americans in Maycomb have little hope that Tom Robinson will get a fair trial. For her part, Calpurnia has placed her trust in Atticus; she is familiar with his beliefs and knows that he is a good man. Her decision in taking Scout and Jem to church demonstrates her ability to trust good people, regardless of their skin color.
So, Calpurnia has a few reasons to fuss over the children. She wants Scout and Jem to look presentable; to Calpurnia, it is a mark of respect to dress well for Sunday worship. She also wants her congregation to know that she works hard and is proud of performing her duties well. Last, but not least, her entrance with her well-dressed charges in tow is also a statement: Calpurnia is proud to be associated with the Finch family.