Note that not all incarnations of Scooby Doo are quite so skeptical; I recall being stunned when I first came across one of the series ("The 13 Ghosts of Scooby-Doo"?) that featured actual supernatural horrors.
I have three theories:
Some of the later Scooby Doo writers retained the innocence of young children when watching the original Scooby Doo, and simply never noticed that "moneygrubbers making fake monsters to mess with the heads of naive victims" was the pattern of that ficton.
Fake monsters catch fewer eyeballs than real ones, more eyeballs means more money, and the newer Scooby Doo writers were themselves moneygrubbers making fake monsters to mess with the heads of naive victims.
The newer Scooby Doo writers were infected with incurable post-modernism, and the behavior described in (2) was a deliberate bit of performance art, with the actual cartoons relegated to mere story-within-a-story status.
I vote #2. #3 gives them too much credit, and #1 not enough.
Although it may not be so much that real monsters catch more eyeballs as that messing with the formula (in a reboot) catches more eyeballs. By now, I've seen enough direct-to-video modern Scoobies that I expect them to be supernatural (as well as inferior in other ways), so maybe next time they'll go back to fake monsters?
Scooby-Doo and the Witch's Ghost is probably the worst. It's not just that the witch is real, which as I said I expect now, but its (positive!) references to Wicca are so unin...
A great column by Chris Sims at the Comics Alliance.
Excerpt:
Tim Minchin fans may recall him mentioning Scooby Doo in a similar light in his beat poem Storm, and it's been brought up on Less Wrong before.
When viewed in this light, Scooby Doo really is like an elementary version of Methods of Rationality.