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).
