That's because most (but not all) USB serial devices use +5/0v rather than +/-12V. Most but unfortunately not all of them are tolerant of +-12V. By the same token, some 12V serial devices will communicate with a TTL serial port and some won't.
Going by spec, it's the TTL level port's fault if they don't communicate, but it's so common these days we might as well consider TTL the standard and 12V operation is a bonus.
The TTL level ports started showing up well before USB was a thing.
Just to make it worse, there are now 3.3V "serial" ports in the wild and some of them do not tolerate TTL levels! That's not good, but at least they are implemented only as header pins on the board and not a 9 pin D.