I'd argue that the explanation for that perception is that big teams are more likely to take advantage of a decision going their way than small teams.
Take Stoke today, they scored from a corner they should have have got, lost anyway, nothing's made of it. If they win that game, even if they win it 3-1, then that's the turning point, that's what the game hinged on. On the other hand, we had a game against Spurs in 2009 where we were 2-0 down, got a dodgy penalty and came back to win 5-2, if that'd been a side like Derby or someone like that, they would probably have still lost 3-1 or something, and nothing would have been made of it. In the same season Ronaldo got sent off at Eastlands because Howard Webb made a technical error as far as the rules are concerned, we won anyway and nothing was made of it.
There's also the fact that bigger a side is, the more analysis there is of their games, and the more refereeing decisions are highlighted as a result. If a small team gets a decision against another small side, there's no coverage of it, maybe one line in a newspaper. United get a potential game changer and it's plastered all over the back pages.
People also let their biases come into it, you know the sort of thing - Howard Webb is a Man Utd fan, he just gave a free kick to Man Utd, that proves it. He disallowed two of their goals? Well that's just to cover it up, it would be too obvious to give them EVERYTHING.
The problem is that the analysis of football is so unscientific, so subjective, one can come out with this sort of shit and because one's coming out with it in a crowd or on a forum filled with people who share the same biases, it gets reinforced and it makes one think it is the reality. It's a real shame, because it brings into question the integrity of people who are doing an extremely difficult job, puts them under more pressure, and they can't defend themselves from it.