I first saw the film when it was released in 1977 and I made an immediate connection with it. I definitely experienced awe and wonder at the massive rolling cloud banks hiding the source of flashing lights in the sky. From the otherworldly clouds, to the mountain illuminated with alien light, to the "city" descending from the sky, there is actually quite a bit of "Biblical" imagery in the film. So I was able to relate on some level to Roy Neary's mania to discover the truth. I agree that his treatment of his wife and family was selfish and tragic at the narrative level, but my analysis is aimed at a deeper level and is more about spiritual hunger, hope and fulfillment. For example, I wouldn't characterize his meet up with Jillian as running off with another woman. Though he does kiss her, and I don't excuse that (again on the narrative level), I didn't read the kiss it as lustful or romantic. It feels like just part of his emotional reverie as he steps through a door that fulfills his great desire for the transcendence represented by the alien visitation.
Spielberg does not consciously have any Christian metaphor in mind as he weaves this story, and I don't have any reason to believe in real aliens from other planets. But I do find some spiritual truth in this story that touches me and makes me reflect every time I see it. As humans we all have Roy's need for spiritual transcendence. We all sense that something bigger than us, even bigger than our imagination, is out there waiting to be discovered. We've had those experiences that give us a glimpse of our lost state, and a hope that it could be recovered. These moments are what C.S. Lewis defined as "joy". The basic message that I take from the movie is that you're not stupid to believe in these things and pursue them, in fact, here is a story where the objective truth of one man's desire, not only revealed itself, but came to get him and take him "home". Spielberg's fictional plot devices might be very different from our objective truth, but like ours, the object of Roy's desire reached out and drew him in. I had the real sense that the creatures who surrounded Roy, eager to touch him and lead him into the mothership, genuinely loved him. Roy abandoning his family seems reprehensible on one level, but in our lives, there are truths that sometimes cost us everything to uphold. In reality, God does not call people to leave their families and again, I don't want to excuse Roy the character, but as a spiritual metaphor, he can be seen as one who is willing to follow the call of God wherever it leads. As the mothership rises to John Williams' majestic score with the "When You Wish Upon A Star" motif, I can't help but imagine God's plan for someday ushering us into the Kingdom where "we will know even as we are known", and I'm left with a vague understanding of what that will be like. I don't expect everyone to react to the movie that way, but some of us do, and I'm sure "we are not alone"… Get it? :-P