. . . No incumbent president has ever been defeated in a primary. And the only “close calls” came in a tightly bunched historical period (1968, 1976, 1980) characterized by substantial transformation of the regional bases of the major political parties.
(Emphasis mine.) Here is the Wikipedia entry concerning the race for the Democratic Presidential nomination in 1980, between Jimmy Carter, Ted Kennedy, and Jerry Brown. It tells us that Kennedy won in Alaska, Arizona, California, Connecticut, Massachusetts, New Jersey, New Mexico, New York, North Dakota, Pennsylvania, Rhode Island, and South Dakota. As for Brown, he won Michigan.
And of course, one of Yglesias’s commenters points out this.
Other than these exceptions–numerous though they are–Yglesias is absolutely right. No incumbent President has ever been defeated in a primary.