I have only read the first three books (of four) in the Eragon series, because after reading the second one with its redundant, verbose, and generally pompous writing, the annoying Mary Sue Arya, Eragon's perpetual moaning about his back (at least ninety pages of the book could have been removed if he didn't complain about his back so much), and not-so subtle borrowing from Star Wars, I couldn't justify spending money on the series. I read the third one when I friend loaned it to me, and I didn't think that I got nearly as much enjoyment out of reading it that the time I put into it warranted. Honestly, these books would be much more bearable if an editor had reduced their length and forced Paolini to stay away from the cliches that choke his work like weeds.
Anyway, I would say that I don't remember anything really problematic in the first book, but in the second one, the elves (whom Paolini encourages readers to idolize) make it clear to Eragon that they don't believe in God (or gods) and several stale arguments against religion are hashed out. In a better book, that might not necessarily be a reason not to read, but this book doesn't have an interesting plot or intriguing characters or deep themes, so there is no point in reading the author's atheistic views.
In the third one, I think that, in the beginning, Eragon performs a really spiteful act of violence against Sloan (the village butcher from the first book) which makes me lose any sense of sympathy for Eragon, and Eragon seems to take too much joy in the books endless battles. Roran also gradually morphs into a character that seems to love fighting and killing people, and that was a shame because, in the second book, I felt like the Roran plot was much more real and exiting than the Eragon part, but in the third book, even that bright spot was taken away.
I would recommend that you encourage your son to read books that are better written and filled with less vengeful and bloodthirsty characters who don't advocate atheism. I would suggest the Dragon Rider series (which Paolini stole a lot from) or some of Brian Jacques' books.
God bless you and your son.