There was a rumor going around the peloton that the descent of Stelvio would be neutralized, but communication to teams was bad and some heard it and others didn't. As a result of some teams thinking it was neutralized they didn't race it, some even came to a stop at the top to put on jackets. Quintana along with others attacked on the descent, or carried on through it and then started pushing the pace when they saw they had a gap may be more accurate (the motos and race officials didn't make any moves to tell them that they weren't aloud to attack either). Thinking the descent was neutralized, Uran and others made no move to chase him down. And as a result he had 2 minutes by the time the descent ended.
Some feel it was unfair to take advantage of the confusion to gain time, it's a complex issue though. Some other factors in opposition to the idea that it was unfair what Quintana did, could the riders see the red flag? A red flag doesn't mean anything in cycling, why did Uran (or others) not just chase after anyway? Communication to the riders by RCS was bad and not everyone even heard the message that was sent out, RCS's official statement after the incident was that only the first 6 turns of the descent were neutralized.
Here's a couple other threads where you can read some of the debates that have been had on this.
http://forum.cyclingnews.com/showthread.php?t=22366
http://forum.cyclingnews.com/showthread.php?t=22349