Lets take a hardware synth for example, The Virus. You can run that straight into the computer via usb, or you can take the analog outputs, run them into an audio device and run that into the computer. A heck of a lot of users prefer running into an audio device over connection via usb - the theory being that the virus analog outs add a touch of 'something' to the sound due to its D/A conversion at that stage. Obviously a lot of it depends on the audio device you're running into too.