Jump scares have a place in horror. The problem is not with jump scares themselves, but their over-use. Good horror follows a basic formula in the emotions it tries to induce in the player/viewer/reader: Tension, Dread, Terror, and Catharsis.
First, you want your audience to feel tense and uneasy... not outright afraid, but a little on edge. Then you want to ratchet the sensation up to Dread. You want them to know that something bad is about to happen, but you don't want it to happen right away. You want to keep them on the edge of their seats, wondering when it will happen and what exactly it will be. Then when the bad thing happens, you move to Terror, the visceral feeling of total panic. This is where jump scares can come in handy. After the peak of Terror, however, you need a trough - Catharsis - to let the audience calm down and get their bearings again. Then, you just repeat the cycle: build tension back up, give the audience something to dread, terrify them by making it happen, and then allow them to cool off with catharsis.
A game that relies too much on jump scares is trying too hard to stay at the peak of Terror, without understanding why the peak is important. Further, while jump scares are a quick and simple way to induce Terror in your audience, their are other, arguably more effective ways to do so as well (being chased by or hiding from the monster/bad guy comes to mind).
Then at the other end of the spectrum, you have games that rely TOO much on atmosphere, where it's all tension and creepiness, but never any payoff... and that atmosphere will be completely destroyed the moment the player realizes nothing bad is ever actually going to happen.
So, in short, the humble Jump Scare shouldn't be written off entirely, but it should be used sparingly and only when appropriate.