There are a few reasons:
1 - Kevin Craft is relatively weak at throwing the deep pass. He just doesn't have a big arm. Consequently, defenses play relatively tight against the Bruins' offense and don't worry too much about Craft going over the top.
This makes it more difficult for Craft to operate in the short game most of the time.
But, the two minute offense can coincide with the defense dropping back a bit. Stanford (and Tennessee, if I recall correctly) were concerned that an end of game deep ball could beat them, so they played deep. This opened up the shorter passes for Craft.
2 - Craft throws pretty well on the move, both on designed roll outs and when he improvises. In the two minute offense, when defenses rush fewer guys, he either has time or he has the room to move around:
So, the combination of facing defenses dropping back and also rushing fewer guys makes the two minute offense suited to Craft.
The more I watch him, I think Craft is a tough, heady kid with some physical limitations. If he had Cowan or Olson's arm, he's really be a good quarterback. As it is, he's getting better.
As a fan, I'm starting to really warm up to him.