Just to be clear the fan is NOT a PWM controlled fan, its a normal 12V DC fan with a tachometer feedback line. My two options are to rectify the PWM to get a clean DC signal OR pulse the DC fan with the PWM signal. Assuming Hero999 understood me correctly, then the preferred method is to simply amplify the PWM signal to pulse the fan?
Hero666 is right, "Don't try to filter the output to power a fan, it will reduce the efficiency and defeat the whole purpose of using PWM."
Since you have chosen PWM to select a particular speed (not the most efficient use of your supply, but you wanted to experiment with the 555...), the purpose of PWM is to deliver controlled amounts of current to your motor. Having from 0V to 12V (supply) provides you with the maximum range of currents available to you (which is the whole point of the MOSFET, in this case).
The problem with inertia is overcome through a gradual increase in the PWM rate before fixing on to a final value (ideally, you would like the current RMS gradient to ramp up initially). The problem with hum is overcome by selecting a frequency low enough to make the energy transfer to the motor as efficient as possible (your DC motor is most efficient at 0 Hz and resonates at certain frequencies depending on its physics) or selecting a frequency above the audible range (or at any frequency that suits the particular physics of your motor).
As Shafri said, you seem to be confusing duty cycle with switching frequency. You can have whatever duty cycle you like at whatever switching frequency suits your motor. It is just a case of switching the MOSFET on for n cycles and off for m cycles (though I am not sure how this is being achieved with the single 555 so far).
My first instinct would have been to use an MCU, especially since you mentioned PWM and tacho-feedback, but if you can do it for less money and complexity with a 555 then I would be interested to know how it turns out!
.o:0|O|0:o.