Good subject!!
Muting is simply one of a guitar players tools - in fact there are a few styles of muting, as well. It is something I use regularly. I too have guitars with wonderful sounds, and I love to hear those tones ... and in fact muting helps me to experience all the rich sound qualities of my guitars.
You may not wish to do it because you don't like the style, or you prefer to play unmuted ... but it is commonly used especially by acoustic guitar players to create an effect. I'll bet you have heard it much more often then you realize, and don't even recognize the more subtle mutes as mutes, because they are done effectively - other times muting is obvious.
An obvious example of muting from my guitar playing is when I finger pick a folk blues tune, and wish to accentuate a bass note. I will commonly strike that note very hard with my thumb (maybe even strecthing the time a bit and hitting it almost late) and mute it with my palm to deaden the tone. The result is an audible 'thump' - the power with which I have hit it makes the sound slightly sharp - and the whole thing gives me precisely the sound I was looking for!
An example of the less obvious muting from my playing (and I am sure many many other guitar players) is when I am flat picking a blue grass tune. I love the sharp, percussive attack of a string that is struck with power, but want to acheive the clear tone and long ring of an unmuted string. What I do is strick the string very hard with my flat pick (sometimes even twisting the pick slightly to get that extra grinding sound)and closely afterwards barely touch the stirngs with palm at the bridge. The result being a loud sharp percussive guitar note of the primary string I am picking, with no buzz or sharpness to the pitch, plenty of sustain, and the fringe benefit is that the other strings I have hit (I ususally hit a few to catch some of the chord at the same time) produce a more muffled ring behind the note picked. Best of both worlds. It is not as difficult to accomplish as it sounds.
Anyway - this may be more than you bargained for regarding muted strings! I suggest you think of it as one of the tools in your tool kit. Try a few muting techniques, and then listen up to your favorite pickers. I guarantee they are using various mute techniques more than you (or perhaps even they) ever realized!