It's much more complicated than the idea that "communism was popular in the South." Following the Geneva Accords, there was to be a general referendum to reunify the country. However, according to the Pentagon Papers, "it is almost certain that by 1956 the proportion which might have voted for Ho—in a free election against Diem—would have been much smaller than 80%." Now this is due to a variety of reasons, stemming form both Diem's actual popularity (not to be confused with his supposed popularity which was greatly inflated), and the recent purges and agricultural reforms that resulted in food scarcity in the North.

The 1954 partition and subsequent moving of populations north and south also changed the dynamics of both countries—in the South, Diem gained a large voting bloc of Catholic and other refugees who were markedly opposed to communism. In the North, significant numbers of political operatives (later to form the backbone of the National Liberation Front), were ordered to stay behind by their cadres in order to sow agitation against the Southern regime and also give legitimacy to the idea that the conflict was nothing more than a civil war.

Now to get to the meat of your question, "how the South viewed communism," that's actually hard to answer because like the North, the South did not permit an entirely free press and censored political thought in opposition to the regime's position (though to a much lesser extent than in the North to be fair). While many in the South before 1968 would have been much more sympathetic to communism as a whole, that sympathy was clearly quashed by the time of the Tet Offensive, where many major towns and cities were attacked and seized by the National Liberation Front, who had hoped that the civilians in these places would rise up and join them. That plainly did not happen, and when the reports of the Hue Massacre began to emerge, it largely hardened the population against the North and communism.

By the end of the war, this fear of a communist bloodbath would reemerge as the North Vietnamese army swiftly captured South Vietnamese territory and hordes of terrified civilians clogged the highways fleeing further south.

For further reading about the breakdown of the Geneva Accords and the reasoning of both the North and the South to violate the accords, I'd recommend Volume 1, Chapter 5, "Origins of the Insurgency in South Vietnam, 1954-1960," specifically Section 1, pages 242-69 of the Gravel edition of the Pentagon Papers.