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I'm an author, so I understand the desire to defend your book baby. But I still think it's in bad taste no matter how politely you go about it. Trying to change a reader's opinion by kindly explaining why their review is wrong, is not going to work. Because I understand the way the author feels, I ignore their reply. But not everybody will. Some people will get upset and that can only lead to all kinds of nastiness which will serve no good purpose for the author or their work.
I didn't like your book. Doesn't mean it's a bad book. Doesn't mean you're a bad writer. I just didn't like your book. And nothing you can say is going to make me change my mind. Let it go. Every book has negative reviews. Twilight has negative reviews. Harry Potter has negative reviews. So does every blockbuster book ever. So think of it this way, you're in good company.