If it's a regular checking account, with no overdraft, the bank loses nothing from having a person like that as a customer. The only money they can use is their own that they deposited there.
In US banking, many customers are relatively costly, with low balances, requiring branches with expensive people to service them. Overdraft happens often with them, and is a cost to the bank. They cannot be given credit, and are not otherwise candidates for other services by which banks make money. So fees- overdraft, deposit, withdrawal, desk usage, account- it is.
It is an optional service, one that is highly profitable ($billions per year for each of the large banks), and one also that arguably best serves the customer's interest, as not making a payment in most cases is far worse for many reasons for the user than making the payment and getting charged a service fee.