Terms of Carriage/Fare Rules are actually quite important. I absolutely do check things like change fees, reroutability, fare class, etc. when I buy a ticket, and will often pay the 5% premium to get a more changeable ticket.
This is much more like reading the tech specs for a new laptop (does it have a linux-supported wifi chipset? discrete graphics?) than a EULA.
A useful fact you may not know: most "legacy" carriers will interline you onto another airline if they can't accommodate your scheduled travel -- for instance, if they cancel a flight, they will put you on another airline's flight if it will get your there faster. This is a VERY BIG DEAL internationally, where they don't always even have daily flights -- if a flight is canceled, it could be 2-3 days before the next flight with the same airline to your destination. Low cost carriers (e.g. Southwest) won't.
that's an aside. the point is: they told him to check-in. their system is flawed. they took the time to hire someone to program the ability to cancel the whole flight, but they ignored the part where they tell him to check-in. to make things worse, they treated him terribly when he tried to and didn't realize his "mistake."