3.9 is the 4690k's turbo clock. If the cpu senses the headroom to run faster it will go upto 3.9 on its own, if the cpu starts to run too hot it will clocks itself down.
definitely. If you don't have an aftermarket cooler it will overheat and damage the processor. But isn't it just using the turbo boost to be at 3.9? Cause that is the turbo boost frequency of it.
Out of the box, your i5-4690K will turbo up to 3.9GHz on its own when lightly loaded (e.g. only 1-2 cores are busy). This is normal operation. If the chip starts to overheat, it will clock back down again. What are your temps? You can use a program like HWMonitor or CoreTemp to tell you. If you are not overclocking (manually selecting a higher speed and/or locking the CPU at a higher speed), the stock cooler should remain sufficient. If you want to overclock, select an alternate cooler from the list at http://www.tomshardware.com/faq/id-2478892/alternatives-hyper-212-evo-budget-cooling.html