I am not necessarily defending them and certainly know that, as an ex-Civil Service organisation, they will be riddled with inefficiencies, with respect to both costs and "work-ethic"!!
However, compared with my profession, their costs are not over the top and you get more for it! That is my point. When I qualified in 1991 as an ACA, I had to pay £500 for the privilege of joining (I did get the handbooks then but have to buy them each year subsequently; they are not freely available on the net). So I am not sure where you got the idea of professional organisation giving discounts!
Sure, life's a bitch but any wannabe (as I am) should know about the charging structure of licences etc before they get to the point of completing their application. The other point that is being missed here is that you are equating each charge with it's actual cost plus mark-up. It doesn't work like that anymore than your Road Fund Licence pays for the upkeep of roads and your National Insurance Contributions pay for your pension! Yes guys, consider it a tax if you like but there ain't no point in whinging.
Don't forget that, as a commercial pilot, you should get tax relief on the licence application (unless Gordon Brown has changed the rules again to be anti-pilot). Always worth a try; the Inland revenue can only say no.
If you want to whinge, whinge at the Government (or your MP) about the fact that pilot training is no longer tax-deductible - that is the real travesty in cost.
Cheers
Whirlygig