Correct USB to RS 3.3 / 5.0 logic level cable
The ATMega has a wide VCC range, some run at 3.3v, some at 5v. It's pins are not tolerant of an input at a higher than VCC voltage.

The Raspberry PI is 3.3v signal only. No 5v Tolerant pins.

The USB to Uart with 3.3v signal but 5v Tolerant pins means you can connect a 5v ATMega to the 3.3v USB-to-Uart, and the Uart will be fine. The opposite is not true. Connecting a 5v Uart to a Raspberry PI or 3.3v ATMega will not end well.

If you need to connect a two way signal between a 5v ATMega and 3.3v Raspberry Pi, you would want a level translator on the ATmega TX -> RPI RX line. The other way round, from RPI TX -> ATMega RX, should be good, as the ATMega has a (VCC * 0.6) Input Voltage High threshold. In this case, 5 * 0.6 = 3v. A 3v or higher signal will be read as a logic high, which works fine.

Update: I take it you mean connect a RPI to an ATMega through a usb-to-serial adaptor connect to the RPI? Then you don't need to worry about level translation. A 5v or 3.3v USB-To-Serial adaptor will work, since the adaptor is a buffer between the two.