Why doesn’t the infield fly rule apply with just a runner on first?

Because the defense can’t get a double play in that situation if the runner stays put. Either

  1. the fielder catches the ball, the batter is out and the runner is safe, or
  2. the fielder drops the ball, picks it up, and throws to second for the force and the runner is out and the batter is safe.

In either case, the offense is left with one more out and a runner on first. With runners on first and second, the defense can get a double play regardless of what the runners do.