Welcome to Gaia! :: View User's Journal | Gaia Journals

To keep it a secret, some methods:

-Magical means, like in Harry Potter, to keep the fantasy creatures hidden (dragons, for example, are notoriously hard to hide, and it takes---if memory serves---something like a dozen wizards to hide one dragon)
-Technology. The Hitchhiker's Guide to the Galaxy has the Somebody Else's Problem field, which, as it says, makes people ignore something strange because it is, well, somebody else's problem.
-Cutting deals with humans in power/having a human aid to help keep up the masquerade and do things for them (numerous vampire stories, but Salem's Lot has examples of both)
-Forming their own society someplace where humans will not look (in the X-Men comic, the Morlocks hide in the sewers, and in numerous comics and urban fantasies, red light districts, condemned buildings, and other places humans avoid/cannot go tend to become fantasy/supernatural haunts)
-Hiding in plain sight. Twilight does this (albeit poorly), where the vampires walk among humans and more or less hide among them.

Reasons for keeping a society secret:

-Limited numbers. A common fantasy cliche is elves are going extinct, and hiding to preserve their numbers.
-Being able to hunt. Vampires, werewolves, and other such creatures benefit from humans thinking that they are mere superstition and horror stories, and thus can get away with killings a bit more easily, because chances are, the police will think the murderer is a human or an animal, and will be looking for a living, mundane murderer as opposed to an undead/supernatural one.
-Peace and quiet. Maybe the supernatural/fantasy creatures just want to live peacefully without humans bothering them.
-Protection/survival. Again with X-Men, the Morlocks hide because they know they will not be safe above ground because their mutations cause them to be hideously deformed.
-Keeping their own numbers in check. I have a book called The Vampire Hunter's Guide, and there is a section of symbols that vampires use to mark their territory. This prevents certain vampires from hunting in certain areas (like, a vampire of a higher rank can prevent lower ranks from hunting, and there is a mark that more or less means, "Humans are getting suspicious. Leave this area alone for a few generations" ). It makes sense when you are dealing with [near] immortals, as too many in one place taking out the food source and increasing their numbers without giving the food source a chance to recover can lead to some serious problems later. And that is not even touching on the humans catching on and starting to hunt them.

All methods and reasons are story-specific, but those are some of the more common/better explained ones.