First and foremost, highway driving is much much much safer than regular driving. There are no intersections (which cause 40% of all accidents), there is high viability, slow turns, no pedestrians, and a super simple traffic pattern. Autopilot is only doing the "easy" driving.
Second, that 94 million miles figure includes motorcycle deaths. Motorcycles have 34X more fatalities per mile driven. That juices the number of fatalities per mile.
Demographics matter too. Telsa owners are disproportionately older than average (not a lot of teens driving Teslas). They are more educated and richer. These people tend to be safer behind the wheel on average.
Telsa's also have a lot of safety features that should reduce fatalities to way below median anyway.
If you want to test if Autopilot is safer you have to test it against a control group that is the same but just didn't use Autopilot.