Alan Paton was an activist from his early years at university to his founding work as the principal at Johannesburg's Diepkloof Reformatory for African boys. He was moved and concerned about what he saw at Diepkloof, even though his friend and Secretary of the Interior, Jan H. Hofmeyr, had had reformatories taken out of the prison administration and made part of the Educational administration.
While Hofmeyr was still in office--before the National Party won the national election and instituted apartheid--Paton went on an international tour of penal facilities. It was while on this tour that he began Cry, the Beloved Country, with Diepkloof and the boys of Diepkloof ever on his mind as he compared various facilities.
The dominant theme is a complex one that mixes the lives of humans with the deterioration of the land and the effect of this deterioration on the cites and the effect of the cities on humans. These three are all connected in an unbreakable causal chain. Though some critics say the most important link, the starting link, is the deterioration of the land, others say the human lives, which Paton saw in their destroyed condition, are the starting link, the most important link, though the answer to the unexpressed question, "How did this come to be?" begins with the land and its effect on villages, cities, and lives. Consider, Paton wrote papers and articles on urban crowding and the cause of crime among black youth prior to writing Cry, the Beloved (Cry, the Beloved Country, Introduction Part II, 1987 Edition).
For further confirmation of the thematic emphasis being the people the land affected, consider that Absalom would not play the profound role he has, that Stephen wouldn't give the summation he does if the most important link were the destruction of the land over the destruction of the human. Stephen wouldn't muse in summation suggesting that all are blameless for what happens to destroy a son (or a daughter) when they leave the shelter of the village, except for the city itself, which carries all the blame.
In light of this, the most important theme of Cry, the Beloved Country is how an environment can choke the reason and life out of an individual and lead to that person's imprisonment and death. This is true in a literal sense, as the novel demonstrates, as well as in a metaphoric sense. This theme, then, is underscored by this metaphor: the deterioration and destruction of the land is the metaphor for--as well as the cause for--the deterioration and destruction of human life.
In conjunction with these is the important complementary theme of the deterioration and destruction of the village and village life and unity. Therefore, the dominant themes are the deterioration and destruction of human lives, the city, the village, the land. Paton supports these themes in another metaphor in which "land" represents the earth along with the people and their culture in his "Notes on the 1987 Edition":
It is a song of love ... informed with longing for that land where they shall not hurt or destroy ... where there shall be no more death, neither sorrow, nor crying, for the land that cannot be again .... It is a story of the beauty and terror of human life, and ... it cannot be felt again. ....
In this quote, you can see the causal relationship between all parts, and you can see the underlying metaphor that equates land with earth and simultaneously with people and their villages or cities, thus supporting the complex dominant themes.