Ooh, Michael Wood might have something to say about that! Surely whether you decide that the basic natural plot points of the story are fictional or historical, both views are equally based on assumption? The archaeological record arguably back up the general shape of the story after all.
Even if you accept there definitely WAS a Troy and there WAS a war between it and the Greeks, there is still no evidence, or indeed reason, to think the characters of Helen, Paris, Achilles, Hector, and various Greek deities actually existed. It's pretty much like saying that Inglourious Bastards isn't fictional because there actually was a World War 2. The movie 'Troy' seemed intent to hoodwink the audience into thinking it's a historical epic by removing all the supernatural elements and adding a few hacky subplots (Achilles' cousin, Achilles' slave girl who conveniently falls in love with him) to grease the wheels.
On the subject of Jesus, despite the lack of direct evidence, it seems more likely that there was a chap in Judea around 30AD with that name (sorry Biggy), rather than the likelihood that the Christian founders were completely pulling everything out of thin arse. Doesn't mean he was God, or even that he did or said anything all that memorable so, as far as I'm concerned, the historical Jesus isn't that important. I'd like to see a proper, literal film adaptation of the Gospels, with Jesus killing fig trees and being shirty to everyone.