What you are seeing is an image noise -- random fluctuations that affect sensor pixels and cause them to measure value a bit above or bit below light that actually comes to the sensor.

The main factor that increases noise is how much is the signal from sensor aplified. There are two things that influence this:

1. Size of sensor pixel: if you have 12 megapixels on 24×16 mm APS-C sensor, each photosite is smaller that it would be on say 2 megapixel APS-C sensor. Therefore is catches less light and needs more amplification. Similarly, 12 Mpix D90 sensor has significantly larger photosites than 12 Mpix compact camera sensor, and thus has less noise. This is one reason people buy DSLRs instead of compact cameras.

2. ISO setting on camera. Basically, ISO says how sensitive you want the sensor be, so higher ISO means more amplification. You'll find that lower ISO settings produce less noise in images, and on D90 noise probably won't be noticable at ISO 200 or so.

Obviously, avoiding noise has it's drawbacks, because larger-sensor camera are bigger and more expensive, and using lower ISO might means either opening up aperture and losing depth of field -- provided that you have fast enough lens (fast lenses can also be expensive). The other option is longer exposure time that means risk of blur from camera shake or moving subjects.

Sometimes, as rfcusa notes, in 12 Mpix images certain amount of noise only matters when you're examining it in 100% magnification on a computer. Unless you intend to produce huge prints, these viewing conditions happen very rarely.