The iTunes App Store is nearly two years old, and Apple still has not published a clear set of guidelines about what type of content is and isn’t allowed inside apps. That’s a problem, especially for publishers eying the iPad as a potential platform for the future of publishing, and it’s an even bigger problem for readers.

We in the press don’t know to what extent we can retain our editorial freedom in the App Store. Working with Apple’s current opaque policy, we’re left to trust that Apple will do the right thing. And time and time again, Apple’s App Store reviewers have been proven fallible, as recently shown by the rejection of Mark Fiore’s Pulitzer-winning cartoon. Apple rejected the toon because it “ridicules public figures,” and after coming under fire in the press, the company approved the app. But in reversing its decision, Apple still did not make its content policy clear.

Instead, the Fiore episode raised more questions. Does it mean we can now publish satire? Or does it mean we have to win a Pulitzer in order to publish satire? Or does it mean we have to stir up negative press in order to publish satire?

The fact there are so many questions points to a paramount concern: Readers don’t know what they could be missing when they’re reading the iPad edition of a publication, as opposed to its print or web version.

The issue is poised to grow as more iPads sell. To understand, you have to consider the logistics of embracing a new publishing medium such as the iPad. Media operations must integrate digital tablet production into their infrastructure, and it’s neither easy nor inexpensive to obtain the software developers, designers and content creators to make such a transition. And if advertisers invest more money in the iPad version of a publication, that pressures publishers to give priority to resources allocated to the iPad.

Given Apple’s lead in mobile, the rate at which Apple and the App Store are growing and the wild enthusiasm among advertisers lining up for the iPad opportunity, it seems inevitable that Apple will to some extent have influence over the content that publishers produce.

Tech observers have correctly compared the App Store to Walmart, which refuses to sell musical albums carrying the Parental Advisory tag. Walmart has even suggested that artists change lyrics and CD covers it deems objectionable. Given the retail chain’s position as the world’s largest music retailer, many agree Walmart has altered the way the recording industry creates albums.

The major difference between the App Store and Walmart, however, is that the RIAA has published details about the Parental Advisory program. Apple has not published such documents regarding content for apps.

Following the Fiore incident, the journalism industry is slowly waking up to my forewarning published in February about the potential for Apple to take control of the press. The Association of American Editorial Cartoons published a letter on April 22 asking for Apple to support free speech.

“The Association of American Editorial Cartoonists calls on Apple to immediately stop rejecting apps because they ‘ridicule public figures’ and are deemed ‘objectionable,’” the association wrote. “Now is the time for Apple to welcome a vibrant and diverse world of news and opinion with open arms.”

Columbia Journalism Review’s Ryan Chittum expressed his concerns about the rejection in his editorial “It’s time for the press to push back against Apple.”

“If the press is ceding gatekeeper status, even if it’s only nominally, over its speech, then it is making a dangerous mistake,” wrote Chittum. He makes an extreme suggestion: Yank apps from the store until Apple agrees to give publishers complete control over their content.