It is all about signal to noise ratio...
All pickups have noise, active pups have less. If you have a very small signal going to the amp the noise that is inherent in the pickups will be amplified the same as when you have a large signal going to the pre amp... The noise will sound louder because the signal is closer to the noise floor.
The other end of the specturm is also true. If the signal is larger than the pre amp can accept the signal is distorted and you have noise again. This is the way an overdrive or distortion pedal works as well, the signal is magnified to the point where the pre-amp distorts the input to the power amp. The later might just sound a bit nicer.
Ok so where do you want to run your pups level? It all depends on the pups and how hot they are... That means how much gain they have. If you have very hot pups the pups raise the level to the pre amp very much. These pups also produce the tone of the guitar much better, but has a greater noise floor. My PRS' pups are so hot that when I dont play anything they give off a constant hiss... I manage by turning the volume off when I dont play anything, the tone however is out of this world... What you would generally want to do is run the pups as hot as possible without distorting the signal to the pre-amp. This will reproduce the most realistic tone from the guitar.
