[thejeff]

The Hobbit was a bedtime story for his kids that wound up tying itself into the mythology he'd been working on for years.
The mythology grew, at least partly, as background for the languages he invented, being primarily a linguist.

I wouldn't say hidden messages, he despised allegory and such things, but that doesn't mean there isn't meaning behind the surface. The Lord of the Rings is deeply informed by his Catholic faith, without being overtly religious, a trick not that often pulled off.

Even more so in the Silmarillion mythology. For example, the origin of the orcs is left unclear because he kept debating with himself whether they had free will and were thus redeemable.