I rewatched the episode last night and I was struck by the High Sparrow's genial humility act: one that Cersei seemed to buy on sight. The Sparrow is the head of a new movement, with plenty of followers who have arrived in King's Landing, and Cersei thinks she has his measure, because it suits her to believe that. And yet, her own cousin and former lover Lancel has made a point of telling her that he has made a full confession of his sins...including their adultery and his part in the regicide of Robert at her behest, and she brushes him off. The High Sparrow has the goods on her, and can have her arrested and tried as he chooses. If he knows about the regicide and the adultery, it's a sure bet he knows about the incest as well, as well as Tommen's bastard-birth.
Cersei is truly not a player...she dismisses Lancel's confession, because she thinks he's a lightweight. She can't put 2 and 2 together and figure the top Sparrow has enough ammo to have her executed. As for Tommen, what's his kingship worth, as a product of incest, or for that matter, Margaery's crown as well?