I don't think it's only the New York Times that uses honorifics like "Mr.," but it certainly is a distinctive trait of that publication. I think some newspapers that carry Times newswire articles will drop the honorifics from Times articles, but I'm not sure of that.
I usually like to be addressed as "Joe," and often ask children to call me that when their parents would like me to be called "Mr. Offer." But when people are trying to get money from me for something, I think it's very rude for them to address me right off as "Joe." When I was a government investigator, I always addressed people with honorifics. I would have dreamed of doing it otherwise.

-Joe-