Source: Have private pilot's license and flew the Shadow 200 TUAV for the US Army. It is a VFR rated airframe that is flown 100% IFR, by nature of it being an ~11ft x 3.5ft x 2ft drone.
How many of those VFR flights have/use autopilot during their flight, I can't say, but basic autopilot systems for GA planes have gotten pretty affordable, so I would expect there's at least hundreds of flights any given day where a VFR pilot engages an autopilot during the flight.
The main difference is that none of those VFR flights are big airliners with hundreds of passengers. For those who don't know the difference, an oversimplification would be VFR = pilot is 99% in charge, with very little assistance from air traffic controllers outside of special controlled airspace, IFR = controllers are giving the pilot very detailed instructions for the entire flight. And it's pretty much one or the other.
[0] PDF: https://www.faa.gov/air_traffic/by_the_numbers/media/Air_Tra...