There seems to be a mismatch here between the article linked in the previous BoingBoing story, and the rule document linked in this story. The article says that the fees will be increasing from $2.50 per leg with a $5 cap for a one-way trip to $5.60 per leg of a trip. But from what I'm reading the rule document states that the old rules were $2.50 per enplanement and changing to a $5.60 per one-way trip.
So right now if I fly from Pittsburgh, to Buffalo, to Rochester, to Midway, to Topeka, to O'Hare* I'm paying a $5.00 fee, as long as each stop is less than four hours. If my stop at Rochester is more than four hours, that divides the overall trip into two one-way segments and so my overall fee would be $10.00. Under the proposed rules, my fees would be $5.60 or $11.20 respectively.
Reading the rules document, it seems the TSA has always interpreted a one-way trip as a series of flights with stops less than four hours in-between. So am I reading this wrong, or are lots of other people?
* I was actually offered that flight once as a cheaper alternative to flying direct from Pittsburgh to O'Hare.