Designing a MOSFET circuit for low pass filtered PWM operation and with saftey considerations
As Andy correctly points out (+1) you are driving the MOSFET into a power dissipating region by adding the filter and its getting warm. The Capacitor C1 is holding the voltage long after the pulse has turned off and will discharge (slowly) through R1 and R12.

To make the MOSFET switch OFF quickly you need to discharge the gate-source capacitor. A much lower resistance for R12 is required. Also the 10k input resistance (R1) will charge the gate capacitor more slowly - as the gate is essentially a small capacitive load you need a small resistor. 

24V supply, 12V fans:

If the fans are all the same type you could drive them in series/parallel so that they only see 12V each. This will also reduce the maximum amount of current the MOSFET needs to handle. 

Now you can run your PWM speed control up to 100% without worrying about exceeding the voltage/current on the fans (or if you just want to run at full speed/turn off just use a digital I/O line)

Overcurrent protection:

Simplest way is to put a fuse in series.