I believe that Sci-fi should primarily be encouraging or thought-provoking. It's my impression that most of the doom-mongering falls under the "thought-provoking" banner. It is a common device, however, to use misfortune or bad situations as a crucible from which something better is able to rise, but the bar for "bad situation" has been set so high that I imagine many people feel that if they aren't destroying the universe with rampant, unchecked, seemingly unbeatable technological horrors, that they can't compete with the ones who are. It's the whole "strength through adversity" trope.

Even ST:TNG, which was on the whole a fairly doom-light series, had its phases (Borg) when things got darkest just before the dawn. ST:DS9 was almost completely defined by strife (as was B5). And these are some of the more popular and extant examples of the genre most people have to look to.