It's usually because the scene has a dynamic range higher than what you camera image sensor can capture. In such cases, if you meter at the sky to have it nicely exposed and captured as blue, the other much less bright subjects will be under-exposed and captured as too dark. If you meter at the other subjects to have them nicely exposed, the sky will be over-exposed and captured as blown out whites.
To avoid this, you need to choose the right time (so that the brightness of sky and the ground subjects are not too large. E.g. certain time of the day when the sun is 45 degree high behind you and lit the ground subject brightly.) to shoot.
E.g.
When I reached the scene at 8.30am, the lighting condition wasn't ideal : The sun was shinning lowly from the front right side into the sky and the subjects on the ground were mostly in the shadows. So I knew the dynamic range was too high to capture the foreground and sky properly exposed at the same time and so I took a total of 4 shots at different exposure (using +/- EV), using a tripod and keeping the aperture and composition constant, with the intention to use HDR merge in photoshop. 2 of the pictures are as below. 1st one is to expose the foreground properly, inadvertently causing the sky and clock tower (lit by the sun) to be blown out white. The 2nd is to exposre the sky properly, unavoidably resulting in the foreground to be under-exposed.
#1 (F/8 @1/36) & #2 (F/8 @1/158)
Later on the same day when the light condition was more ideal at 4.45pm, the sun was coming about 45 degree behind me from my left and illuminating both the foreground and the sky very well and the dynamic range of the scene was within what the camera's sensor can capture. Both of them were properly exposed with a blue sky captured in #3 below :
#3 (F/8 @1/359)
Time of the day is very important as it determines the lighting condition and dynamic range of the scene. For the above, in order to capture the lush greenery, I should have arrived much earlier than 8.30am, before the sky became so much brighter relative to the foreground.
If not, you would need to use filters to cut down on the scene's dynamic range.
Alternatively, as Zcf mentioned but usually only possible in static or landscape scene), take a few shots of the same scene with a tripod at a few different exposures (3 to 5 different settings) so that each of the subject in your picture has been captured as properly exposed in at least one of them and then use photoshop HDR to merge them.
Read this thread :
http://forums.clubsnap.org/showthread.php?t=209830