In considering Tolkien’s works, consider the following:
1) No hidden “Christian” messages (unlike many of the author’s discussed by others above, e.g. C.S. Lewis)
2) While it’s based on European folklore, all theological aspects are deleted, and it has become the pattern for a significant genre of secular fiction. If one rejects Tolkien, one pretty much has to reject a large amount of western literature. Whether one should reject literature is a different issue – one could argue against all fiction, but that would mean the issue of which fiction doesn’t arise at all.
3) Tolkien was very clearly anti-Nazi, well before the war, and at a time that the British establishment had yet to decide what it thought of Hitler (his correspondence with a would-be German publisher as whether he was “Aryan” make that very clear). For some authors, such as Jules Verne, even if the book has no “Jewish aspect”, one probably needs to remember that the author was involved in anti-Semitism movements of this time, and these movements eventually led to the Holocaust (or at least to decision of many in France to collaborate with the Nazis).