Without telling us what type of commute you have. (Traffic, City, Highway Stop & Go) I'd would have to guess thatI you're riding includes a lot of sitting in city traffic or slow speed stop and go driving. This will cause the temperature will increase and the fan will run. Since, I believe, you are not running a turbo'd K-bike, it doesn't matter if you let the thing run until the fan turns off or if you just turn it off. BMW K-bike motors are about as close to a standard car motor as you can get. Basically they are a car motor and can and will take a whole lot more use and abuse than pretty much any other m/c out there. Unlike a turbo Saab that could, on the rare occasion, be stubborn if you don't let the turbo wind down, a normally aspirated K doesn't care.
You may consider giving the radiator a good cleaning to ensure optimum airflow and heat transfer. If the antifreeze is old, replace and if it really bugs you add a manual fan switch (tapped off a keyed power source).
