The Case Against The Case Against Auto Increment in MySQL

In the Pythian blog today, John Schulz writes The Case Against Auto Increment In MySQL, but his blog contains some misunderstandings about MySQL, and makes some bad conclusions.
The Concerns are Based on Bad Assumptions
In his blog, Schulz describes several concerns about using auto-increment primary keys.
Primary Key Access
"…when access is made by a secondary index, first the secondary
via Planet MySQL
The Case Against The Case Against Auto Increment in MySQL