This reminds me of the BBT show with the nerds talking about giving Wolverine a prostate exam. When talking about comics, there are no silly questions. However, I’d think that air resistance and terminal velocity in this case are irrelevant. If the Flash has the capability to shed heat then why would air resistance bother him. His biggest problem is propulsion. He gets his speed from running and at some point he loses friction that enables him to continue to propel himself. On another note, many years ago a fool had himself strapped to the top of a Boeing 727 to see what would happen at higher speeds. The 727 took off and cruised at 170 mph. The guy survived but was unconscious. Since we are talking about a comic book being, I don’t think that is an issue.
The application of real world physics to comic book abilities probably leads to a better understanding of science than only applying science principles to the real world, because you’re actually taking time to figure out the subtle effects that science principles have.