In the anime it's clearly said, that every one sees the chakra of the Nine-Tailed Fox as red/orange, when Naruto uses it. But no matter what chakra Naruto uses for his Rasengan, it's always blue (like normal). Why is this?
Naruto's own chakra color is blue, which contrasts with the Nine-Tails' own chakra color of red.
Interestingly though, despite Naruto using the Nine-Tails' chakra to create larger and larger Rasengan, the color remains the same. This might be a plot hole; this may be indicative of Naruto himself performing the attack with a larger amount of chakra under his control.
Shinobi have chakra that is blue. naruto was not using the kyuubi chakra for the rasengan hence why it is not orange/red.