You're right. Toyota dominated. They didn't let the others stand a chance.
The others weren't perfect. They stopped more, or at the wrong time. They had a set up that let the tires go off. Or couldn't set it up to cope with the bumps. Or the drivers weren't so amazingly consistent. All these little things added up to being 0.76% worse. Or 2 laps.
Or they were Peugeot.
Remember those years races when Audi beat others despite having a slower car. Imagine what happens if someone runs like that, but all the cars are pretty equal.