I agree with you in general about the fee, but remember that there IS a cost for the FFL to handle the transfer. While calling in the information may be free, the FFL is responsible for keeping the paperwork for the next 20 years. And it must be available for inspection or to help with a weapons trace, so it can't just be thrown in a storage unit somewhere, it has to be relatively easy to find a specific form by either name of buyer, date, serial number, or any other identification that the ATF may use to request information.
If we look at a FFL that does say 25 transfers a day (I'm not sure what a reasonable number is, but I would bet that is somewhat reasonable for a large shop taking into account both busy and slow days) you're looking at something like 180,000 forms that need to be filed and easily retrievable. There's a cost to making that happen (floor space, filing cabinets, creating a system to track everything, etc...).
Is $50 or $25 the right number? I don't know, but handling a transfer isn't free for the dealer.