From 2009 the APD will be abolished and airlines will be charged based on a new formula based on aircraft emissions, NOTE AIRLINES WILL BE CHARGED not passengers, of course the goverment in the run up to the election will put positive spin on this for customers, but airlines will pay more and will have to decide how and if to pass this on, either way HMG will get the dosh whether the aircraft goes full or empty and MOL and other bandits will no longer be able to pocket the cash that rightly belongs to the passenger.
This is not really that big a deal.
The airlines that choose to slap fees on any refund of taxes are those who generally operate with higher load factors and therefore are less susceptable to the new tax given that it will be spread over a greater level of ticket yield. Effectively this is now a tax on seats with every seat, be it full or not attracting a form of taxation.
You say that airlines will be charged and not passengers however this is currently the case with the airlines acting as the tax collector on behalf of the government. Make no mistake about it, the airlines will not be 'paying' the tax on your behalf. You will be charged through the cost of your flight ticket, of that there is no doubt, although this new method is likely to be far less transparent resulting in you potentially being charged more than is actually being levied by the government for your particular seat on the aircraft. Essentially this charge will just be re-grouped into what most airlines class as 'taxes, fees and charges'.