How the heck do airlinesdo it?

In the next couple days I have to buy tickets for my mother-in-law and her son to go back to South Africa for a visit. She adopted him when she lived there after retiring as a teacher. They now live back in the USA.
Usually tickets run anywhere from $1600 to $2300 round trip. That is Minneapolis, MN to Joburg. The preferred route is MSP to ATL then ATL to JNB. The ATL to JNB leg is 18 hours but beats flying to Europe then down. Delta has the ATL to JNB flight.Airfare makes no sense. My local airport is Duluth , MN. All flights from here connect into MSP. Usually they charge a $150-300 premium to fly the 45 mins from MSP to DLH, but there have been times when I have found the price to be cheaper to fly from DLH than MSP.Last month a friend had to take a quick trip to Florida to pick up a car. He used frequent flyer points. They wanted 25000 points to fly out of MSP, but to fly from DLH thru MSP they only wanted 15000 points.
It makes no freaking sense.Next week we are going to Puerto Rico. Flights from Duluth, on Delta, were $1200. $900 from MSP. I got tickets on Sun Country for $530.
The best way to buy plane tickets is to start early and shop around.
Kayak.com does good comparisons and you can adjust a lot of variables to nail down exactly what you want

That is the one my mother-in-law prefers. That way she does not have to make the connection in Europe. I don't understand her reasoning, because I think it is easier to clear customs at final destination rather than clear customs in Atlanta, then have to deal with luggage again.
I have not taken that one. My wife and I have flown through Amsterdam. Didn't mind it. 8 hours from US to Schipol, 3-5 hour layover in Schipol then 11 hours into JNB.Last time I booked them they had to fly through Paris, because the ATlanta flight was $500/person. I'll start looking today at her options.

Like most things in life, it ain't that simple.
One explanation.
Air Fares 101 - Why do fares change all the time? - CheapAirEdited by Theodoric, : No reason given.