In the article he basically describes how his profits were swallowed up by marketing expenses. I wish he had broken down in more detail the $50,000 in royalties from his other traditionally-published book since it was such a drastically different deal for him

"After selling more than 11,000 copies in its first year, The Heart to Start has earned a little more than $3,000 profit. That’s a barely twenty-nine cents per book.

By comparison, I’ve sold about 16,000 copies of my traditionally-published book, Design for Hackers. That has earned nearly $50,000 in royalties (plus at least twice that in related course sales)."

later:

"Here’s the basic breakdown of my earnings and expenses for the first year of The Heart to Start:

    Copies sold: 11,374 (3,099 were free)
    Total Royalties: $19,173.31
    Fixed Production Costs: $431
    Advertising: $15,422.60
    Total Profit: $3,319.74

"