I think the "triviality" of paying the back wages and the "triviality" of the fine are directly related to each other. $40K / (7.25-1.21) = 662 underpaid hours [1], or put into probably an even better unit for comprehension, 16.5 man-weeks or 4.25 man-months.
This is bad, and in particularly bad in a very revealing way. However, it's not like this was a sweatshop employing hundreds for months without detection, which I suspect the mental model people are reading into this story. While I suspect 3.5K is a bit low, the millions upon millions that I suspect many people are emotionally calling for would also be inappropriate.
[1] Forgive me if I don't fully spell out the units here.