Well, it's not unlike what happened with Batman Begins. Christopher Nolan didn't know Batman all that well, but it didn't matter since he had David Goyer helping him come up with the story and write the screenplay.

The Goyer to Abrams' Nolan on Star Trek (and the sequel) is Roberto Orci.

All Hollywood ultimately cares about is that the director is competant and can handle a big-budget movie, especially when we're talking $150 million or more. Occasionally, the director also happens to be a huge fan of the property in question. Zack Snyder made Warner Brothers a lot of money with 300 and used it as his chance to finally get their long-in-development-hell Watchmen movie greenlit. Even then, Warner chose to co-finance the movie with Paramount, knowing it would be twice the budget of 300 and once again R-rated.

Scott Pilgrim is a good example of a low-budget adaptation with a geeky director that Hollywood was willing to make since it wasn't a huge financial risk. Compare that to something like Land of the Lost, from the previous summer (and also from Universal), also with a geeky director but with a bigger budget because of the box office potential Will Ferrell's name carries.

This is why I think Joss Whedon never would've gotten the job for Avengers if it'd been a Hollywood studio calling the shots and not Marvel. Handing a $220 million summer tentpole to a guy whose only movie cost nowhere near as much and couldn't even make that back at the box office??? Well, I think the studios will be a little more willing to take a chance like that after seeing how it worked out for Disney.