Autofocus sensors are essentially complex arrays of light-sensitive strips, and pairs of strips can detect when focus is "out of phase". Some sensors only detect phase shift in one direction, some in two, some in two diagonal directions, each with successively higher sensitivity to contrast differentials and more phase sensitive strip pairs in various arrangements. To my knowledge, AF sensors are simply tonal in nature, and do not factor in color. This is in contrast to metering sensors, which these days on prosumer and professional grade cameras, usually DO factor in color and possibly a variety of other factors. AF points also usually only "see" a fairly small area of the overall image frame, and as they are designed to sense phase shift, targeting an AF point on a surface of relatively uniform color (regardless of what that color may be) is unlikely to produce enough phase shift to lock onto and adjust focus, or if at most start AF hunting, but lack the necessary contrast to lock focus at a certain point.
While AF sensors effectively see in monochrome, and see an entirely different world than image sensors or the human eye sees, they likely have similar color-sensitivity ranges. (If there is any kind of filtration, either deliberate or as a result of the materials used in the AF sensors themselves, they may have unconventional color sensitivities as well.) Most photo-sensitive devices are less sensitive to blue light, and to some degree red light, than to "middle" colors, such as yellow, green, and very light blues. That could introduce less sensitivity to contrast within those color ranges. I wouldn't suspect that such differential in sensitivity would affect AF nearly as much as a lack of contrast at the selected AF point, but it may have an impact in some cases.
The key to AF is focusing when the AF point is very near areas of high contrast. The edge of a dark figure skater against the bright ice will likely lock every time, where as the center of the dark figure skater is likely to result in a bit of AF hunting until it locks onto something, and that something may not actually be what you intended. Using multiple AF points can assist in locking AF somewhere useful, however it broadens the area factored into AF, and its entirely possible you will still lock focus on something you did not intend.
It may also help to understand how the AF system works, as there is a world of variety in AF modules, and they all offer different capabilities. I recently researched the AF capabilities of a lot of cameras while debating whether or not to get a 7D. The D90 has a decently advanced AF system that has the ability to predict and track subject motion while focusing. If I remember correctly, its motion detection and tracking work differently depending on whether you are in a single-shot or continuous-servo AF mode. In single-shot mode, I do not believe the D90 will actually lock focus on a moving subject, and will wait until the subject has stopped moving to actually lock focus. In servo mode, the D90 will track the subject that it believes is in focus, but as far as I can remember, there is no actual focus lock since the camera is continually adjusting focus so long as the shutter button is at least half-way down. If you are using single-shot AF mode, you might not be getting AF lock because your subjects are moving. You might want to try switching to continuous-servo mode and see if you have more success with getting in-focus shots. I would offer that this is much more likely to be your issue than the color of your subjects. The D90's AF system is quite configurable, and I believe there are ways to "tune" it (for lack of a better word). You might want to hit the D90 manual or do some research on how to control the D90 AF, and see if you can get it working better for the way you use it.
For reference, here is the article I read on D90 AF (the article states D200, however the AF module is the exact same one):
Understanding the Nikon Multi Cam 1000 AF Module
