I agree with original poster that investigative journalism is dead, for the most part, as far as the mainstream goes... but the Onion satirizes things every single day and I've never seen it actually mess with intelligent people's curiosity about real findings in science. Ignorant people stay ignorant because it's comfy there, while those who are actually curious look further for information.

Also, keep in mind that academic communities (biology, physics, psychology, etc.) operate almost completely outside of the domain of journalism. They publish their reports in peer reviewed journals and it goes on to influence further research and changes technology, etc. The academic community doesn't need every regular Joe to believe in or even really care about its recent discoveries.

The real problem is not that The Onion exists, but that people don't think to question their own reality naturally. That's a problem that has always existed. In any era throughout history, the majority of people have been snug as bugs not being truly curious about a single big question ever.