Plot hole: During the Congressional hearing, it is suggested that the alien signal could have been faked from a satellite - as Ellie only has her own experience to go on, it leaves her believing what happened, but still with an element of doubt. However, as a professional astronomer, Ellie would have immediately dismissed this since a simple parallax (triangulation) would have confirmed that source was at the distance of Vega - a distance far too great for any rocket to reach. (This is mentioned in the book). In fact, this is mentioned early in the film, when the employees in New Mexico calculate the source of the signal while it is transmitting prime numbers.
Plot hole: After Ellie makes her journey which she firmly believes happened she is questioned as everyone else watched the pod drop straight down into the water. But no mention is made of the chair that is violently shaken loose during her 18 hour journey. If that were to have happened in the split-second the pod fell through she would have been badly injured more than just a bump on the head.
Answer: If anything, I think the film's producers deliberately left godly topics unaddressed (and questions dangling, unanswered) because they didn't want to alienate any particular audience. However, we know the producers of "Contact" certainly did vilify religion through the sinister scenes with Joseph, the evangelical extremist. At the same time, the film created empathy for the president's glib theological adviser, Palmer Joss. So, I don't think the film was shying away from religious topics, and I think it was pretty fair to the religious viewpoint, for the most part. But this movie wasn't about religion; it was about a primitive, materialistic, self-centered and aggressive species (humanity) reluctantly acknowledging the existence of vastly more intelligent and even godlike entities throughout the cosmos. Even the first-contact entities, advanced as they are, acknowledge other entities much more ancient and much more advanced (the virtual architects of the space/time conduit). The implication was that we live in a universe that may be populated with many intelligent entities that answer every human criteria of godhood. Ellie's narrow-minded atheism was surely shaken to its foundation by her experience; and, while she didn't "convert" to archaic earthly religions, she was spiritually a different person upon her return. The film, however, is open-ended and fence-straddling and doesn't presume to definitively answer the question of the existence of god, leaving it up to the audience to decide.
Charles Austin Miller