It's not either/or. Both are necessary to varying degrees.
Good Horror incorporates both. Atmosphere with no "scares" is like a walk in the park at night. It's unsettling but not scary. Scares with no atmosphere is like someone jumping up behind you and shouting "BOO!", you feel a jolt and a sense of anxiety but 2 or 3 times and your just angry and want to punch the perpetrator in the face.
Someone jumping out of a bush and saying "Boo!" while you are walking in the park at night drastically escalates the horror.
The problem with us humans is that we rationalise things unconsciously. Repetition breeds familiarity. We get used to things. A drawn out segment of creepy music and sound effects in a dark dimly lit *insert spooky place* is fine for a time... until the brain starts to pull you back into reality. Then it becomes a corridor explorer simulator.
Without the physical stimulation that a good fright gives, you become resistant to the atmosphere (a scare you expect but never comes eventually loses its edge). The fright is basically the "pay off" to good atmosphere. It's exciting and distressing. It resets your brain back to "shits scary" again and allows the atmosphere to keep doing its thing.
Excessive or poor use of frights eventually leads to fatigue and frustration, which kills atmosphere anyway.
So yeah, a bit of both is essential to good horror.
[edit]
It should be noted that System Shock 2, Amnesia and Silent Hill have BOTH atmosphere and jump scares.
Remember this guy:
Suddenly appearing through a door you just opened and going "may I be of service" with that faulty synthetic voice before violently exploding is a pretty effective fright.
I would even argue that FNAF has atmosphere and pretty good atmosphere at that. The use of cameras that allow you to track progress of the creatures, the clever use of lighting effects, the not so random noises you hear, the sometimes random freak occurences.
What FNAF fails at is that, while effective at first, the jump scares become repetitious quite quickly. Each night brings a new potential fright which has some influence at diminishing the fatigue, but because the games systems are a little too obscure at first (and feels like it's completely random), you will fail A LOT and that causes a rapid drain on both the atmosphere and scares as it's replaced with impatience and frustration.
I can make the same argument and complaint about slender man.