Not sure how the rattlesnake population is holding up, but overhunting a species can eventually diminish it to a point where its very survival is in jeopardy. Example; alligators in the south east, particularly Florida. Sharks in many parts of the world, in the US, off Long Island and southern New England. Granted, the alligator, after many years of being protected is making a comeback ... but there was serious concern that it had been overhunted to the extent survival of the species in that area was questionable.
But we're talking about rattlesnakes here. Rattlers and mean animals with a serious attitude problem. Most highly venemous snake are pretty mellow and will only strike when they feel threatened. Rattlesnakes are teritorial and will bite you for being in the wrong place at the wrong time.
I'm a big live and let live guy when it comes to wild animals, not into hunting (not against it, just don't feel a need to do it myself) and will generally give animals a chance to get a way without damage. Not with rattlesnakes though, once you get chased down a winding mountain trail by one of these bugger you learn there's no use appeasing them.
And as for the "threat" of extinction, lots of animals go extinct all the time without humans having anything to do with it. It happens. Maybe if we kill all the mean rattlesnakes we'll force the species to mellow out and become less of a threat.