They have to log the weapon into and out of their books. Which admittedly doesn't take long but does acquire them some liability ATF wise. So, that firearm has to pay some amortized part of the FFL licensing which allows them to provide the service of transferring in the first place. If they have a storefront, they have to pay for the rent, lights, heat, insurance, salary(s) etc. Every transaction of any kind has to pay for its share of the total operating cost of the business, in any business.
On a more renumerative level, every gun you buy from somewhere else on a transfer is a gun they didn't sell from inventory or get a bit of profit on.
TANSTAAFL
If they didn't charge something for transfers there soon would be nobody left to do them. As long as there is competition between your local options on costs then there's no unfairness to it.