I think that the cause of your problems can be resolved with the answer to one question: What do your 'not-in-the-cockpit' shots look like? If they're also low in color saturation and contrast, it's your camera. If not, it's the glass/plexi/magic-clear-airplane-stuff that you're shooting through.
I'm going to vote for the window-caused problems as I can distinctly see a reflective artifact running along the right-side window edge that matches the contour of the cabin interior and a slightly diagonal reflection in the center of the shot that could easily be mistaken for a sky feature.
You can try to compensate with the white-balance (as mentioned above) and exposure compensation functions. If you have questions on how to use them or what changes might need to be made, feel free to PM me. You might also try the other suggested remedy of a polarizer, though that would only reduce the component from reflection abberations from one source. Your flash wasn't on in that photo, but it could cause similar results with an added bright spot or starburst in the photo. Even if it's getting dark out there, leave the flash off. Not only will it add reflections to your image, but it isn't powerful enough to add light to anything beyond 15 or 20 feet anyway.
(Personal pet peeve: People at sporting events or concerts in HUGE stadiums who take pictures of the event with their flashes on. Do they really think that little flash can throw enough light out there to make any difference? Save your batteries, people!)
I think that what's happening is probably a combination of coatings and transmission qualities of the plexi designed to improve the pilots' view, reflections from inside the cockpit, and something called 'flare.' Flare is caused by light being trapped in glass as it bounces between the two outer surfaces kind of like in a fiber optic element. That causes the camera to act like there's an slightly opaque grey curtain between it and anything on the otherside of the glass.
On your next flight, shoot a photo of the instrument panel with no windows visible and then shoot one of something outside the window. I'll wager the first is clear and well defined, but the second will look like what you posted.
So, if it is your windows, you have Photoshop or PhotoElements running to your rescue! As other posters have mentioned, you can alter the contrast, saturation, and exposure (brightness) with those programs. That will help make up for the short comings of the original photo. However, someone mentioned having used a quick color enhancement three times. Remember that every adjustment you make will result in a slight quality loss. Making the changes all at once rather than in little steps is much better for your image quality. It might take a little more program knowledge, but you'll be much happier with the results.
Again, I don't want to bore anyone with anything more detailed, so feel free to PM me if you have specific technique, software usage, or camera utility questions and I'll do my best to get your shots 'cleared up!'
Best,
PhotoPilot