Why call a USB connection a serial connection?
As @ratchetfreak answered, USB is a Serial bus. But there is more.

The microcontroller on Arduino boards has one or more built-in peripherals called UARTs, which stands for Universal Asynchronous Receiver-Transmitter.

This is what the Arduino core calls a Serial port. It uses the same kind of protocol as the old DB-9 serial ports on PCs and such, but at 5V or 3.3V logic levels. Contrast this 0V to 5V voltage swing to indicate Logic LOW and Logic HIGH with the RS-232 standard for the old PC serial ports, which use a +12V to -12V swing to indicate such.

But PCs today don't often have the old RS-232 serial port. They instead have the new USB - Universal Serial Bus - port. On the Arduino board is chip that communicates on one side via USB with the PC and tells the PC that it provides the equivalent of the old COMPORT or /dev/ttyS* serial device; and on the other side via UART with the microcontroller on the Arduino board.

It's like we are "emulating" the old PC serial ports in software over the new USB bus, which itself is a serial communication system, though much more complex than a plain UART.