In Alan Paton's note on the 1987 edition of Cry, the Beloved Country, he tells us a story: apparently, when the first two readers of his manuscript, Aubrey and Marigold Burns, asked him what he would call his novel, he challenged them to a game. All three of them wrote down the title they liked on a piece of paper before comparing them. All of them wrote down "Cry, the Beloved Country." The title actually comes from a phrase that repeats several times within the novel. (Check out chapter 11, paragraph 19 for the first time the narrator actually says it.) And we have to admit, the phrase does have a nice ring—it's almost Biblical in its simplicity and depth.
The title obviously has two parts (that comma in the middle there makes it easy to see where the title splits). First, there is the "Cry," which is an order to someone. It's basically saying, hey you! Cry! (And to be honest, we obeyed this order several times when we first read this book.)
The second part of the title tells us who the "Cry!" is addressing: "the Beloved Country." The beloved country is, of course, South Africa. Within the novel, the character Arthur Jarvis, in his work "Private Essay on the Evolution of a South African" talks about the great love he has for his country. And it is precisely because he loves South Africa, because it is his beloved country, that Arthur wants to improve it: "It is only [… when] one learns of the hates and fears of our country. It is only then that one's love grows deep and passionate" (2.24.3).
Arthur Jarvis's emotions reflect the love of country that real-life author Alan Paton feels towards South Africa. He's not writing this bleak portrait of 1940s South Africa out of hatred for the country's faults. Instead (and maybe even more painfully, because it shows how much Paton cares), Paton proves that wanting to reform his home country is a sign of his great love for South Africa, for its landscape, its cultures, and its history. Indeed, Paton writes, in his note on the 1987 edition of the book, that the phrase Cry, the Beloved Country, "was written by one who indeed had loved the earth deeply, by one who had been moved when the birds of his land were singing" (source, Note on the 1987 Edition)—by one who perhaps cannot help but love his country too much for his own comfort in this bleak period of South African history.