Well Blue light is at the higher frequency end of the visible spectrum, so it has a shorter wavelength then red or green light. Although the AF sensor is not sensitive to colour it doesn't actually measure the contrast of the image. Instead it separates out the light coming from either side of the lens aperture (Which is why AF points have a requirement for a minimum aperture to work) and measures the difference between the peaks and the troughs arriving at the sensors from each side of the aperture. Because the peaks and troughs are closer together for the blue light is is actually easier to measure the difference in the phases for the shorter wavelengths, as you only have to move a short distance to be a big difference in the two signals. In the lower frequency, longer wavelength signals the it takes a bigger difference to see a significant change in the output signal.
It is interesting that the AF Assist beam fired by most flashguns is red, as you would think that they would get better accuracy by using a blue light.
Alan