Undertale spoilers
@kara_dreamer@witches.town This is because Flowey earlier, upon agreeing quite enthusiastically to help you kill everyone and everything right at the beginning, realises that the only being with enough Determination to end his existence, is Chara.
This makes him deeply, intrinsically afraid. As a being with Determination, despite his lack of a Soul, he wants to live. Fear gives way to terror and he flees as it implies Chara smiles THROUGH Frisk, knowing this.