I understand it happens rare but i think it does if, for example, Not-PE is Hate Sink and PE is very cool.
For more specific example, in conflict between Cinder Fall (NPE) and Arthur Watts (PE) where majority of viewers was on a side of Watts. Mostly because Cinder already earned fans hate by killing Pyrrha and having blatant death cheating. Watts, on the other hand, was more freshy and competent villain, who didn't became MB only because his motivation is too petty.
Was you ever on PE side in PE vs Not-PE conflict? It's not necessarily has to be a long conflict - maybe one scene/situation.