I just changed the oil in my 06 Silverado with about 90k miled on it when I noticed what appeared to be rust inside the cap(plastic cap). I looked down inside the spout and there looked to be some more rust with some sludge which looked like it was from water. I drained the oil and it looked fine with no water or anything strange looking in the truck. Should I be worried about this??
Yes, you should be concerned.
My first guess would be that this truck is driven mostly for short-distance local errands, as that type of driving does not allow water vapor (a byproduct of combustion) to be evaporated from the motor oil. If this is the type of driving that the truck is typically subjected to, this means that you need to change your oil much more often.
If the truck is not used for mostly short-distance local driving, another possibility is a thermostat that is stuck in the open position, thus causing the engine to run too cold. Also, you should check the entire PCV system to be sure that the valve is operating freely and that the PCV hose is not gunked-up.
You can pop off your valve cover fairly easy on your truck engine, and actually look inside, and see if there really is any sludge. Take some pictures and post those for us to see.
BC.