They ignore it, and they ignore you in it. It is complete protection from Warpers. With care and timing, you can use it to slip by every dangerous point in the game, even without Silent Running and the Shield Generator. With the engine off, it is invisible to all creatures (except, perhaps, in a limited way, crabsquids). It is immensely useful, possibly the single most important piece of equipment in the game.
Those same people probably run the thing on flank speed (the middle one) all the time and burn down their Power Cells unnecessarily. Only people who talk about how useless the Cyclops is are the impatient types who want to 'beat' the game as quickly as possible.
