que is relative pronoum used as a Complément d’objet direct (COD) in the sentence L'indicatif ne contient pas de part d'incertitude. You could rewrite your example as :

Le subjonctif contient une part d’incertitude que ne contient pas l’indicatif.

But, in your example, there is a coma after “incertitude” in order to stress the second part of the sentence (“mise en relief” in French). Because the relative pronoum must be placed directly after the object that it replace, another pronoun (ce) is used before the relative pronoum. In other word, “que” is then the COD of the sentence L'indicatif ne contient pas cela, where “cela” refers to “a part of uncertainty” in the first block.