Black is USB 1 or 2 that runs on the same rail. Red USB is 2.0 on a different line that won't shit out on you if you need to pull a lot of power according to terrible sources. The only time I see red is if it piggy backs on top of an esata so I really don't know. Blue is 3.0.
While I've heard and that the red ports run on a different rail, I don't believe that to be true.
The most likely reason is that the ports are made by different manufactures, and that's it.
USB 3.0 is coloured blue.
My P45 ASUS board has a few red USB ports. I think they just do it for cosmetic reasons.
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