I can only tell you how my Travel Agent does things. She doesn't like the $25.00 fee , but her agency (the "boss" ) requires that she add it to the price of a cruise. After our first completed booking with her, she's taken the fee off all of our other bookings at final payment. (I suspect she's taking it out of her commision.)
As long as they are upfront about it, I don't have a problem with a TA charging a small fee.
"A truly happy person is one who can enjoy the scenery on a detour."