From what I see in the report, the thing that annoys the pilots most is the "do you really need that extra amount of fuel?" question from the dispatcher. The article is clear in pointing out that the PIC has ultimate authority, but that that does not mean the dispatcher can't query the request for extra fuel. Dispatch cannot overrule the PIC, but they can question the need for extra fuel.
Separately, but related, MSNBC also refers to the fuel hedges by airlines, which in some cases come to an end. South West apparently faces an increase in fuel costs equal to its profit in 2007, so they've resorted to flying more direct routes (including over water) to save fuel.
It's not a case of questioning your authority, but a case of giving you as much as you need, not a gallon more. Ultimately if you as PIC are not happy with the fuel amount you've been given, ask for more. Just be prepared to say why.
S.