The rules talk about the "opinion" of the referee. The referee can only have an opinion as to whether the ball crossed a relevant line if he sees it. What I am talking about is a situation where for, example, the ball is going in, and a defender lunges out a foot and clears it. The ref saw the incident, but it happened so quickly that he can't be 100% sure if the ball crossed the line. He then has to decide whether it is more likely or not that the ball crossed the line. The laws do not say that he should think, "well I am 95% sure it crossed the line, but as I have a 5% doubt, I can't give a goal".
You might also get a situation where the ref should give a goal even if he does not actually see the ball crossed the line. Say a shot is looping over a goalie with a defender rushing back to cover. The defender is standing two yards behind the line with his head about to connect with the ball. However at the crucial point where the head connects with the ball the goalie gets in the way, so the ref doesn't see where the actual connection happened. However, as the ref can see the defender was two yards into the goal, it could well be his opinion that the ball must have been behind the line and he would then give a goal.