I think it is fine that some readers prefer the antagonist than the protagonist, however it should not be reproached to the author like that. Also, it does not mean the author did a mistake, it may be simply a personality difference between author and reader.
I often feel closer to antagonists that are non human sentient creatures like aliens or fantasy non human races, for example. I find it is difficult to comment politely to explain that. Sometimes the author get upset no matter how it is explained. But in my opinion the minimum the commenter should do is explain the personal path that made them feel closer/more empathetic to the antagonist, or sinply more interesting, due to the commenter personnal interests and expectations.
Edit: re reading it, the comment you receive can be taken a different way too, as 'when you (=me, the reader) is so weird that...) which is not a critic toward you at all. But it's not very clear.