ATM stand for Automated Teller Machine. In-game, the ATM allows you to make withdrawals from your account, deposit money into your account, or check the balance of your account. The latter of these operations will deduct a fee of five dollars from your account. This fee is removed when using the laptop to check your account, and the laptop will give you a detailed readout of both deductions and deposits into your account.
Caution when using an ATM is imperative. The bank watches your account, and if you deposit a large amount of cash into your account, the bank will contact the DEA and your risk and exposition factors will rise significantly. There is, however, a way around this monitoring.