The electronics in your vehicle can overheat for several reasons, but one of the biggest reasons is running the vehicle with improper gearing for the conditions the vehicle is being run in. For example, if you are running a Rustler VXL (#3707) on high speed gearing (31 pinion/76 spur) with a 3s LiPo and you are playing around in the backyard, jumping, trying to do wheelies and running through grass the amount of stress and strain on the electronics is increased dramatically. Because the motor and speed control have to work harder this generates a large amount of heat within the electronics. The electronics can only handle so much before they overheat.
The stock gearing that each Traxxas vehicle comes out of the box with has been tested to ensure optimal performance for all-around use during normal use.