I think I've only ever once actually missed a flight. I had just moved to a new state and put my drivers license in a different place because I was planning to go to the DMV and get a new one, and then I had a flight and left my passport in the wrong bag and so it was in my car. When I went to check in, I realized I had to catch the shuttle to the valet parking service and come back to the terminal, and I was about ten minutes too late. It was in BDL and I was traveling to DFW (on DL); I waited all day through three full flights (to ATL or CVG) until I fortunately got on the last one of the day. But they didn't charge me - this would have been back in about 2000.
I've known of people who got rip-roaring drunk between flights and missed a connection that way. Can't say I have much sympathy for them, but it happens.
Regarding the story of the student, I'd like to say it's unimaginable that a service business would do that, but we all know they would. It's not like the airline's hands were completely clean.
The practice though that super-ticks me off is charging to standby on an earlier flight. I know it's impractical to track, but I believe that if an airline denies you a seat on an earlier flight and it goes out with empty seats, and they then get you to your destination late, they should pay a huge penalty, no matter if it's Wx, Mx, or whatever. They could have gotten you there but they chose not to.
I wonder if the cornucopia of pax-friendly changes are the industry's way of saying Thank You to Congress for bailing them out. It seems both logical and fair. "We" are paying tens of billions of dollars to keep the airlines afloat; the last we can get is a mitigation of some of the more abusive fees.