The best answer you'll get is "because it's a rainbow."

While its present associations with native Andean culture are strong and legitimate, there's no good evidence that it actually ever was an Inca flag. The best support we have is from a Spaniard named Bernabe Cobo, who wrote, in the 17th century, about an Inca procession with standard bearers at the time of conquest. He claimed that those with the family line of the Incas bore a small square flag with a rainbow. There is no archaeological or contemporary historical basis for this though.

You'll find some attempts to retroactively apply meanings to the colors of the Cuzco 7-banded flag and the square suyu flags, but again, they're post facto and don't have much bearing on the reason for two blue stripes.