Linear control, fan pulsing
You’ve built a current source for the fan, not a voltage source. The inductance of the fan makes this unstable. 

As wired, the collector current, i.e. the fan current, is h_fe times the resistor current, which in turn is the PWM averaged by the base capacitor.  But that only works in the proper V_ce range. 

I think the answer is to switch to a voltage driver.