That's not quite what the article says:
>The agency says it recently charged H211 on a cost-plus basis, and before that charged a standard budgetary price that was infrequently reset but over time reflected the government's costs.
So at least for some time the government was charging a standard accounting price that wasn't updated with rising fuel costs. This won't necessarily compensate over time. If you're smart when the government is below market you buy and when above do what they're doing now:
>Since the fuel cutoff, the Google executives' planes have been coping by flying back to Moffett with extra fuel purchased elsewhere, Mr. Ambrose said.
The reference to cost-plus does seem to imply they fixed this hole at some point.