The "official" reason is that Guggenheim is too busy promoting his latest documentary, Waiting for Superman. The unofficial reason is that his conscience just wouldn't allow him to make the film, the announcement for which was quickly derided by the entire internet. Yes, the entire internet.
Paramount and the Bieber camp won't sweat this much. It's not like 16-year-old girls were screaming about the long-overdue team-up between Bieber and Guggenheim. Frankly, a music video director in tune with this generation might end up being a better choice, if they indeed go with someone like that.
For the record, Bieber hasn't taken to his Twitter account to comment. He's probably just wondering who this David Guggenheimer dude is...