Were dragons real? Think about it, virtually every culture on earth, throughout all of history, has spoken of giant flying reptiles. All these stories can't possibly trace back to a single source. There has to be something deeper going on here.
The obvious problem is we don't find dragon bones. But we don't find the bones of lots of things. The number of unique human fossils could fill a bathtub, and a great many dinosaur species are known from a single bone (including the largest dinosaur ever discovered, which was identified by one bone that was destroyed in WWII in an air raid, and no other bones have been discovered since). Since fossils of anything are very rare it is not at all surprising that dragon fossils are rare, or non-existent.
What if we are looking in the wrong place?
People from all over the world who take certain hallucinogenic plants report seeing the same beings. One commonly encountered being is a man with an alligator head, and this alligator headed man says the same things to everyone. It can't all be a case of suggestion, where people encounter what they expect based on second-hand sources. What I suspect is that these are real non-physical beings who don't look like anything, being non-physical, but they assume a certain form in the mind of the person having the experience out of convenience.
What if dragons are like that? Dragons are not flesh and blood reptiles, they are non-physical beings encountered in altered states. That would explain why they can live for thousands of years, why they are wise beyond the limits of human intelligence, and why they are only encountered at the end of an arduous quest undertaken by an individual who has had specific preparation. What if going out to slay a dragon did not involve a knight suiting up in armor and riding off to battle a dinosaur, what if it involved fasting, and sensory deprivation, and ingesting certain hallucinogenic plants, and then the knight doesn't kill the dragon, the knight's encounter with the dragon allows him to eliminate negative qualities within himself? That is why only particularly pure knights of great spiritual fortitude could go out to meet with dragons, because the psychic shock would be disastrous for a lesser mortal (like a very bad trip). In that sense then dragons are not the enemy, they are the ally.