The article stated 4000 copies sold, and $12000 in income. Math is math, no matter how you look at it. $3 a copy in income isn't all that bad at all.
The author's book was priced at $8.95 according to the article (Kindle version). Perhaps the author should consider price adjustments to see if the market will respond with more sales?
And this all assumes the author did a nice job with their marketing efforts in the first place... because "bestseller" also doesn't mean book sales on autopilot.