Stepper Motors getting very hot after use
The motor current is controlled by the driver. You can set the pot on the driver board to set the current as shown in the datasheet: 



This is accomplished inside the driver chip by driving the coils with a PWM signal. If the coils were powered continuously from the 12V they would burn out because usually they're only rated for a couple of volts continuous. A 12V rated stepper would be objectionably sluggish.

In some applications the stepper current is automatically reduced when it is "holding" position, which helps keep the motors cooler. I don't know if your setup has that ability. In any case if you keep the surface temperature below 60°C you should be fine. If you intend to operate at higher temperatures you should consult the datasheet for the motor.