I'm guessing banks like direct deposits because they create a barrier to the customer taking their business elsewhere. It's nice and easy to have direct deposits and automatic payments set up, but if there's a problem - yeah, it's annoying to have to stop things, and the bank/company you're having a dispute with has no real incentive to expend energy to straighten things out. But a customer with a direct deposit can't just say "I'm taking my ball and going home!" without having to jump through hoops, so is probably more willing to put up with little stuff that other customers won't.
(That's my guess, anyway!)