According to a press release from the Mets:
His shoulder exam was otherwise normal. Johan will spend the next week with the Mets in New York. He will rest from throwing but maintain a fitness program. He will resume his throwing program once his shoulder is at full strength.This is obviously good news. As soon as the news broke that Santana was going to miss his next rehab start because of discomfort, I'm willing to bet most fans were fearing the worst.
As much as I would like to see him back this season, I would rather he just spend the rest of the season rehabbing, and return in 2012. Better safe than sorry.