If you want to dance to the music, you must pay the piper . . .
I appreciate Yip's comments about application fees, to a point. However, I always thought that background checks, recruiting costs, etc., were a cost of doing business, are expensed out come financial statement time, and are factored into pax and/or freight fares. Accordingly, I believe that app fees are a cash cow for at least one or two regionals, especially those which charge $50 to apply (I complained about $15 app fees thirteen years ago.).
I also submit that only the applicants whom the companies intend to interview are sent for background checks. Few are interviewed compared to the number who apply, and pay. I would also submit that the actual cost of these background checks, screenings, etc. is much less than the app fee. Therefore, profit is made, especially on those thousands of applicants who will never be brought in for interviews.
Having said all that, what are you going to do? Not apply? Of course, app fees are wrong, but if you do not apply to companies who charge them you just might be cutting your nose to spite your face. Besides, app fees are tax-deductable if you itemize.
Good luck with your job search.