Apple failed to support Flash in the iPad's web browser even though it's the most widespread format for interactive and video content on the web, and the iPad is touted as the ideal device for surfing the web. Apple's Steve Jobs believes that Flash's days are numbered, and that it will be replaced by the recently developed HTML5 format, which is supported by the browser used by the iPad and other iPhone OS devices.
Adobe adapted its Flash development technology to make it possible to produce applications that would run on the iPad despite its lack of browser Flash support, but Apple updated the iPhone Developer Program License Agreement to forbid that process, blocking Flash developers from the device entirely.
As the Post's source said, the decision has drawn the ire of many media professionals who have made their livings distributing content in the Flash format. They believe Apple is trying to bully the industry into switching to HTML5 by refusing to support it on the iPad. The iPad isn't quite popular enough yet to make that happen on its own, but its siblings the iPhone and iPod touch might do the trick.
The DoJ hasn't released any comment about its alleged inquiry into Apple's Flash policy, but it's already watching Apple closely because of its iTunes Music Store policies, which companies like Universal, Sony and Warner Bros. have accused of antitrust violations.