Magnetic guitar pickups are inductive, and require compensation, although this opportunity is also used for tone enhancement, not just correction. Without compensation, they have a strong low middle emphasis and little high frequency response - overall a very muddy and muffled sound. This is why typical hi-fi Baxandall treble & bass controls are unsuitable.
To hear the natural sound of a pickup, use a typical guitar amp with the middle set to full, and bass and treble on 0. This is actually sets a flat response in the amp (see below), and I expect you will hear a muffled and muddy sound. And that's the whole point of these tone controls providing compensation for the natural sound of a pickup - the middle control simply boosts the pickup's normal middley sound. The treble and bass controls do the opposite - they boost higher and lower frequency levels, leaving a notch in-between for middle cut (see the Fender/Marshall comparison below). So with typical settings of a bit of bass, middle and treble, the overall tone equalisation complements the natural pickup sound for a balanced response of lows, mids and highs.
Read more here: http://users.chariot.net.au/~gmarts/ampbasic.htm