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The only problem with that theory is
A. Spiritual places and magical beings of that magnitude would have to exist. I can't see how magic could work nor do I see a reason to believe that dragons can do such things. Sounds like an awesome idea for books, however.
B. The government DOES hide things from us. However, the only thing they'd hide, if they do at all, would be something that would effect them in a negative way. The existence of dragons would cause them no harm if there were fossils of dragons. Infact, that would be a MAJOR breakthrough in the evolution chain. Hiding the existence of dragons would be no gain to them. If the theory that they maintain dragons and killed them off was true, that'd mean the government would have to be more powerful and more advanced then we could imagine. However, that is not the case. If dragons existed, the government would be destroyed just as we would.
C. For dragons to exist, they'd have to exist at the time humans were humans through the evolution point, so there would have to be a point where humans had to live with dragons. Problem is, our technology back then as well as our numbers would have caused us to be wiped out pretty nicely. Sticks and stones may break MY bones, but dragons dragons can't be harmed by me.
D. Finally, as I have said before, there isn't really any reason to believe in dragons besides the wide tales being said here and it seems there isn't anything backing up those claims.

Exactly. Perhaps they were from another dimension or planet, and the aliens brought them here to show the humans of ancient times. If they brought them back with them, that would explain why no fossils have been found.

A vast majority of things in history cannot be proven at all. 99% of all history books are theories made up of the little evidence we have. Same goes for science. A lot can be proven, but most of what we "know" is just theories.

You know a scientific theory is concrete, right? Germs are a theory, Calculus is a theory, gravity is a theory.

A scientific theory comprises a collection of concepts, including abstractions of observable phenomena expressed as quantifiable properties, together with rules (called scientific laws) that express relationships between observations of such concepts. A scientific theory is constructed to conform to available empirical data about such observations, and is put forth as a principle or body of principles for explaining a class of phenomena.

If theories were concrete fact then they wouldn't change over time. That's why they're called theories instead of laws (even though they are based on "laws").

String Theory is hardly fact. In actuality, there's almost no way to determine if it's true or false (which flies in the face of the scientific method), yet it's still considered a contender for the "Theory of Everything."

Theories help us explain observations; they are not immutable laws.

I would hardly call the "String Theory" a theory, though.
It doesn't use a set of facts to tie an idea together. It was more of an idea that sprung up.

But even if that IS the case, we aren't arguing what theories are, we are arguing of evidence for theories.
That's why I was saying that believing dragons were brought by aliens and taken away could make sense. However, there are no facts, evidences, or anything leading to believing that idea. My point is to show why even believe in it.
Gravity has evidence to back it up. If I kick a rock, it will mathematically fall into place by the forces that act upon it and the medium it is in. That is not only sensible, it is provable.

Forgive me for mistaking with the RELIGIOUS string theory. That was my first thought hearing that. However, the other one I read up still has little backing it up to be called a theory.

Lets screw with the laws of physics shall we?