The ignorance of capitalist economics that is displayed in this thread is breathtaking.
Hands up all those that hold shares in some company.
Now, of you shareholders, how many of you have no objection to your company not recovering those costs of doing business that are easily recoverable?
This is the economic argument for the application fee. It is the exact same argument that applies to "charging for the endorsement". Very simple, and surely very simple to understand.
The issue of whether to charge for such things, and how much to charge, is also governed by simple economics. Think "supply and demand" and things may start to make some sense.
Despite what you probably think, those in charge of airline recruiting are not idiots and are well aware of the effects of such charges. They know how many applicants they have, the quality of those applicants, and how many get all the way through the process. If it should become necessary to enlarge the pool of applicants, such "barriers" will be lowered accordingly.
By the way, it is not necessarily true that an airline will have a higher standard of pilot if they weren't to charge for such things.