Whether airlines raise fees or taxes increase, consumers pay for the extra stuff no matter what. A tax on fuel would be better in that the airlines pay for what they use as opposed to charging customers in advance. A tax on fuel is a better measure of how much carbon monoxide is put into the atmosphere by airplanes in terms of a carbon footprint.
The best way for government to make it appear favorable to the people is to hide the taxes that they pay. This is often done by building a tax into the cost of a good by taxing a component or something which is not directly purchased by the consumer. This is still a cost born by the consumer, however the consumer is no longer aware of it. Consumers should be aware of the taxes they are paying.