First, the conclusion that baggage fees are a good deal doesn't follow since the baggage fee shortfall is accounted for in the price of the ticket. A more valid conclusion is that travelers who don't check bags are subsidizing travelers who do.
Second, opportunity cost is used to conclude that the fees are a good deal. However, most travelers won't travel without baggage and since baggage fees we're most likely just a way to raise prices without raising the ticket price per se, it's a wash.
I suppose it would be different if the article made a case for cheaper, carry-on only flights which sell the cargo space for shipping. Does something like this exist? Seems to be a good business opportunity if not.