See, that's just it. Tolkien outright denies the allegorical nature of his work, but that only means that those picked out by the observant were unintentional, not that they don't exist. People find themes of conservationism, the dread of war, and the hope of faith. And these make sense, as Tolkien himself was a Roman Catholic environmentalist who lost most of his young friends in World War I. He can't claim with honesty that his writings were not influenced even in the smallest way by the important notions which hold sway in his life.
But here's where any reason to obsess over it falls apart: sure, you can champion the so-called Christian themes (humanity suffering under the lordship of a fallen yet superior despot--Sauron--and his fell band--Nazgul, Orcs, et. al.; overcoming temptation out of dedication to an ideal; the setting apart/sanctification of the Fellowship; the crowning of the king at the dawn of a new age; etc.) of the work, but that requires one to also deal with the clearly occultic themes (the garnering of powet through talismans--the rings; use of "magical" arts to direct actions and do battle; use of runes as basis of most languages within the work; superior created beings who physically and directly interact with and among mortal men while imparting gnostic insights of another realm, a "spirit" world; etc.) that can be seen side-by-side with them. In fact, I know many Christians who would not approve of the books/films for this very reason. Then again, they probably disapprove of Masters of the Universe, too, so I don't necessarily hold with them on that.
In the end, it's totally unimportant. People read into things what they will, but, so what? It has nothing to do with it as taken at face value. It's just something to talk about and keep something going. And that's a given in any group of devotees, whether the LOTR fandom, Christians, and particularly a combination of the two. But it's no reason to get bent out of shape over it, either. Yes, such themes do exist, but they aren't really important in any meaningful way.
