This quote is a metaphor, a figure of speech in which a comparison between two unlike things is made without using like or as for the purpose of creating a deeper meaning. Here, the comparison is between Opal's father and a turtle.
In this scene, the preacher (Opal's father) is listing for her ten things about her mother for her to remember. When he mentions that number ten is "that she loved you very much," Opal responds, "But she left me." When her father replies, "She left us," Opal sees him as a timid turtle, who rather than facing his problems head on, simply retreats into his shell and hides from things. Opal wishes her father would be more courageous, more of a leader, and simply stronger as a person. The betrayal and confusion over her mother leaving, and this view of her father is a premise for the entire story, which is why Opal feels so lonely, and why Winn Dixie makes such a wonderful companion for her.
I thought that she was comparing her father to a turtle. In that she thought he lived his life in a shell