A very logical explanation I'd agree. And in most cases true. But let me go into some details of how a Low-pass RC-filter works.
How a capacitor works -:
A capacitor is nothing but two conductive plates separated by a non-conductive di-electric medium. For. e.g, in PIO caps, the paper is the "plate" and the oil is the dielectric. When a DC current is applied across a capacitor, positive charge builds on one plate (or set of plates) and negative charge builds on the other (by the principle of induction). The charge will remain until the capacitor is discharged. When an AC current is applied across the capacitor, it will charge one set of plates positive and the other negative during the part of the cycle when the voltage is positive; when the voltage goes negative in the second half of the cycle, the capacitor will release what it previously charged, and then charge the opposite way
How the filter works -:
You basically have a resistor-capacitor combination with the capacitor in parallel with the load (Vout). So now, the entire signal will pass to ground either through the capacitor or through the load. At lower frequencies, during the positive swing of the input signal, the capacitor has plenty of time to charge to (almost) the input voltage before that charge is "removed" by the negative swing. Hence the entire input voltage is seen at the pin of the capacitor which connects to the input (and to the load as well). Hence, the capacitor pin connected to Vout develops full voltage across it due to the time the capacitor gets to charge, which the load sees.
As we increase the frequency, the capacitor gets less and less time to charge it's positive plate (the one connected to the input and output) and consequently lesser voltage is seen on the load.
This charging and discharging characteristics of the capacitor in relation to the frequency bring about the frequency filtering characteristics - and in this topology, is what enables this scheme to act as a low pass filter. The high-pass operation can be explained similarly.
How all this mind-altering crap relates to tone -:
In a guitar whose pickup signal which contains a wide range of frequencies, It's precisely this charging and discharging characteristic which results in different kind of capacitors having different tones. We can see now that it's not a question of whether the capacitor
lies or not in the signal path. It works by, simple speaking,
subtracting frequency components of varying amounts (amplitude or voltage) from the input signal, with the amount subtracted depending on it's frequency. Hence it's functioning will affect whatever signal is
left for the load to see.
Different materials will have different charging characteristics apart from the time they require to charge (uneven charging, non-standard frequency response etc etc) which will this result in changes to the output signal also.
PS : Electronics experts (including my profs) will take exception to my liberal usage of words like subtract, left over signal....these terms are technically inaccurate but in the context of the discussion, put across the point well.
I better change the tip before I solder any caps then, I think mine is about 5 years old! ...and soldering heavy speaker wire. 
