My interest rate is maybe 0.3%, so they're definitely making money on that.
But that's not a "fee." Obviously banks cover their operating expenses somehow. That doesn't mean they charge me to have an account or to deposit cash (in fact, charging for deposits would be counterproductive).
They do it directly or indirectly, I don't know how US banks works but usually over the world bank accounts vary accounts with no/low fees give low interest and vice versa.
Maintaining ATM's and counting and transporting cash costs money, cash isn't free I don't know about US banks specifically.