Funny story - during my stint in Grad School there was some sensitivity to how each person wanted to be referred to.
All Post-Docs insisted on being called "Dr." rather than "Mr."and all tenured Profs on being called "Prof." rather than "Dr."
Non-tenured Assistant Profs had the worst choice get called Dr. and upset themselves or get called "Prof." and potentially upset the people who could grant them tenure :)
Guess which one they choose?
In certain geographic and/or certain academic circles leaving out the 'dr' is, depending on how you look at it, a newish kind of snobbery or a recognition that getting the PhD isn't all that much of an accomplishment. Not putting emphasis on the 'dr' part is like saying 'of course everybody who matters has a PhD, no need to mention it every time'.
It's the same reasoning as why one wouldn't list a driving license as an accomplishment when one is a professional race car driver - 'of course' everybody who is somebody in racing has passed their driving exam a long time ago.
(the same comment was mentioned in the comments to the OP - I was quite surprised nobody mentioned my above reasoning, I thought it was common knowledge by now).
"Mister" is correct for any adult male. They may prefer the more exclusive title, but that's no more obligatory than my preference to be addressed as "Captain Awesome." And some style manuals (including the Associated Press Stylebook) actually forbid "Dr." unless the story is about medicine and the person in question is an MD.
People with Ph.D.s are not that frequently called Dr. Also, if there is one source that I am pretty sure would know how to refer to professors and Ph.D.s, it would be the Chronicle of Higher Education.
That being said, it's also uncommon to specifically use Mr. (except for male surgeons, of course) - not unknown, but uncommon. I'd have less of a problem if the article was about, say, his dog having a funny coat pattern or him complaining about parking restrictions at the local council, but it is weird that in an article about his professional conduct and capacity, that the lesser title should be used.
Mr. is still not the correct formal title for someone with a PhD, Dr. is. The only exception of this is when dealing with patients in a medical setting where the degree could be confused with an MD. (I'm still having flashbacks to addressing wedding invitations 7 years after the fact).
Chronicles of higher education might have a different publishing standard, but I'm not sure why they would.
This wikipedia entry seems to indicate that it is common to address someone of his stature as "Dr.", with the possible exception of perhaps in social settings where doing so might cause confusion (with MD).
