At the end of the movie dozens and dozens of abductees are shown leaving the spacecraft. The 13 US Navy airmen were taken from their lives in on Earth only to be returned 30 years later. With Roy Neary the aliens implanted such an overwhelming desire to go to Devil's Tower that it completely disrupted his family*. They violently ripped the child Barry from his mother's arms. All these seem like pretty malevolent actions. Yet, they are seen as wondrous. I would think many would see the aliens as a threat but I didn't sense any of that in the movie.
Has Spielberg or any of the writers [Hal Barwood (additional story uncredited), Jerry Belson (written by uncredited), John Hill (additional writing uncredited), Matthew Robbins (additional story uncredited)] IMDB cast and crew discussed how they squared the circle of the aliens being seen as benevolent when their actions seem pretty malevolent?
*I know Spielberg said he would not make the same choices with the Neary character if he had made the movie later in his life.
Close Encounters of the Third Kind was made when Spielberg was a young man. At the time, he did not have a family like Roy Neery does. The story was a kind of escapist adventure that he thought a downtrodden, trapped, middle age guy might want to experience. He has since said that he could not make Close Encounters at this point in his life because he would never make the choices that "he" (as Roy) did in the film.
SFF Stack Exchange question Why did the aliens choose Roy Neary?
