It's never inappropriate to thank someone for their time and thought. Reviews certainly take time and thought. And the fact that a thank-you isn't obligatory or expected--especially if the review was negative--just makes the gesture that much more appreciated.
I also think it's appropriate to take the opportunity of a thank-you note to address negative aspects of the review in a professional and non-confrontational way...and certainly to draw errors to the reviewer's attention. One of the authors of a book I reviewed sent me an immediate (and sincere) email thanking me for presenting my negative comments as matters of taste with which other readers might disagree, and then politely mentioned two minor errors I'd made--one in my transcription of a poem excerpt, the other more complicated. Since the review was published in an online venue, I was able to contact the editor and perform damage control within a few hours of the review's appearance--a win-win-win situation for reviewer, reviewee, and readers.
On the other hand, a vindictive little tantrum disguised as a thank-you note would not have gone over as well.
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