Tire life, speed, fuel. The majority of Mclaren's laps were 3.5 seconds + slower than Hamilton's, he was lapped twice..... twice. Even at a 1:33 second average that means he finished over 186 seconds behind, over 56 laps that is well over 3 seconds a lap slower. He actually finished some 207 seconds over 56 laps he averaged being 3.7 seconds slower per lap.
it was a stupid race really, should have been two stop, it was fuel limited but Kimi/others went much faster while on softs largely because more grip means faster cornering, gain fuel efficiency by braking less for corners and maintaining a higher average speed. Rosberg was pushing within the context of being fuel limited and tire life/pit strategy likely effected overall speed. Rosberg sped up, then was over his fuel target, and slowed back down. Again the fastest in race lap was 1:30.9, qualifying was a 1:26.4 was it. An in race lap of 1:33... is meaningless, in qualifying with fresh tires, no fuel, and no fuel saving the Mercs were 4+ seconds faster, the Mclaren was less than 2 seconds faster.
It's also being suggested that once they knew a point was out of the question and they were fairly certain the race was over they turned up the engine as much as possible and pushed harder for the last 2-3 laps. I'm not sure how true that is, the more likely situation is that going so slow he had more tire life left than anyone and they realised they had extra fuel on board at the end of the race because there would be 2 laps less to do... so just put his foot to the floor harder and braked later into corners, apparently he was coasting into a lot of corners for fuel reasons... which again points to very little electrical harvesting/usage.
Either way, the average race pace behind was woeful, the speed at the end wasn't good enough and either they turned the engine up... and the speed sucked, or they threw fuel usage out of the window due to fluke circumstances... and speed wasn't good.