Many Japanese people place importance not only on the individuality of characters but also on their meta-roles. Therefore, the statements "Naoya is a villain" and "Naoya is a character who plays an important role in proving the overthrow of male chauvinism" are compatible.
Naoya is popular in Japan because he is a "male-dominated man who is defeated by a woman." Japanese people are satisfied with the ending that Naoya embodies and highly value his character. In other words, Japanese people who are happy about Naoya's defeat are not male-dominated.