The reason is never explained directly in the episode, however there are a couple of pertinent pieces of information given:

 - the space plane the astronauts are testing is said to have
   disappeared from radar for a short period during it's flight
   
 - the space plane crashed in the desert and the astronauts were rescued
   from the wreck

The episode leaves the viewer to guess what might have happened to the astronauts to cause them to slowly disappear - did the spaceplane cross into some other dimension during it's absence from radar, and now they are gradually being drawn back across? Was there an encounter with aliens or a some natural force which is causing them to fade away from reality? Did they all die in space, or in the crash and death is coming to claim them?

Rod Serling, who wrote the screen play based on an existing short story, [later commented][1] on this episode:

> “When Dick Matheson first wrote the story, it had nothing to do with
> astronauts. At least if I’m dealing with outer space, I can say
> something, someone [caused the disappearances], and I’ve got a little
> bit more going on.”

So the his intent seems to have been to leave the cause deliberately vague whilst focusing on the ever increasing desperation and confusion of the unfortunate protagonist.


  [1]: https://thenightgallery.wordpress.com/2015/03/17/serlings-re-zoning-efforts-and-when-the-sky-was-opened/