Journals such as AMTD and ACPD contain an open discussion where anybody can comment on papers under review. The peer-reviewers are still anonymous, but other people commenting are not. If I'm reading a paper and have questions about it, what are the pros and cons on posting them as public comments versus writing an e-mail to the author directly? On the one hand my comments may improve the paper; on the other hand, if I write something stupid or step on somebody's toe, that may harm my future career.
What do others think?
(Edit: I might add that in the case I have in mind, I am already in contact with the author)
The first advantage that comes to my mind is that emailing the author and getting an answer will only help you, while commenting on the paper and getting an answer in the open discussions might help other readers as well.
But I really understand your concerns. One does not want to embarrass oneself or the author.
Which leads me to the inconclusive result of
+1 for both methods.