Board Thread:General Discussion/@comment-25208022-20140808150050/@comment-4224349-20140812005445

Koldun007 wrote: Why else would he toughen him up and not simply let him relax? In order to make sure he could be the next guardian of the portal and continue his research for him.

Stan's toughening up Dipper for when the world fights back. But, in the newer episodes, I believe that he's doing this for when Dipper fights the zombies or fights the shapeshifter he's prepared, thanks to Stan. Stan wanted Dipper to not find anything out about the town since it's crazy, but just in case he's preparing him.