Martin waited for the two Sky guys to be on the front. I think Thomas wanted to chase (I'm sure he could have won, as all Sky riders never get tired), as you can see him quickly switch hand positions, ready to shift and chase. But because it was Martin, who would take the responsibility of yellow away from Sky (and all pacemaking duties), he let him go. In fact, in the post race interview, Thomas said as much, that he let him go.
So, yes, the group, if they were all working together, could have probably gotten back to him, but all of the above factors, plus Giant was probably all spent, he was able to get away.