One thing the gain control does not do that a guitar volume pot does is affect tone. Rolling off the guitar volume will reduce the treble coming from the guitar a little. Unless the guitar has active pickups and an onboard preamp, that is.

The capacitor+resistor “treble bleed ” circuit some guitars have across the volume pot to let some high frequencies pass unaffected by the volume pot can reduce this a bit but it still happens (and can be useful).

The DAW gain control right at the “front” of the virtual channel is mostly for setting up the gain so the audio is at the desired level when it hits the first plugin/eq. If you’re working in 24bit+ (and who isn’t?) the track faders are fine for mixing purposes without quality loss.

Worth noting that the knob on a guitar doesn't actually do anything special to "clean up" the distortion. All it does is reduce the output level coming from the guitar, the same as the gain control does if you pull it down into the negatives. Turning up the gain control gets similar results as you would from putting a clean boost pedal in front of an amp or perhaps replacing your pickups with higher output pickups that sound essentially the same otherwise. 
 
tlw's point is correct that the wiring of passive pickups also tends to bleed off some of the highs which helps to reduce some harshness but the main impact of the guitar's volume knob is the change in output level.
 
What I like to do with amp sims is put an EQ first and then use the EQ's gain to control how hard I hit the simulated amp. By increasing the EQ output level/gain, I can simulate a guitar with hotter pickups. By decreasing the level and some treble, I can simulate rolling off the guitar's volume knob. This gives me the flexibility after the recording is done to play around with a hotter vs. tamer guitar tone without having to re-record with different guitar volume levels or a different guitar. 
 

Thanks everyone, I learned a lot hearing how each of you uses the gain knob and that's a great idea Dave76 Thanks for the tip.