Which fan is this? If you want the fan to always be on, you can just wire it with the input from the power supply so that it gets a constant 12V when the printer is turned on. No need for the Arduino to control the speed.
If this is a fan cooling your prints, then you don't necessarily want it on all the time, especially for the first layer or two of PLA or when you are printing ABS.
If the fan is cooling the fins on your hotend, then it is a good idea to have it on while your hotend is hot. However at least Marlin code should have an option under the configuration_adv.h file for turning the fan on at 100% when your hotend is above 50 degrees (default). The fan will also continue to stay on after the print is completed until the hotend cools down to less than 50 degrees.
Not sure about the configuration_adv.h settings for cooling the stepper drivers. In that instance my fans are also stopping and starting somewhat randomly.