The red dot is the lightest side of the tire. it should be mounted with the dot lined up to the heaviest side of the wheel (usually the valve stem) so it will balance with less weight.
Most tire shops are smart enough to align the dot with the valve stem. Unfortunately it's not that uncommon to see car tires and occasionally bike tires mounted without following the protocol. Brand name tires today are normally require very little weight to balance. The only advantage to aligning the dot and the stem is the potential to minimize the weight needed to balance. If they needed minimal weight to balance the tire it's kinda a so what deal. Clean the dot off if it bothers you and ride on.