Had it been a best-of-three set match, Stepanek would have won, having claimed the first two sets. Over the longer format, however, Murray's superiority came through: he is ranked number two in the world against Stepanek's 148th place.
Quality is more likely to be evident in the longer-run than in the shorter. The outsider might pull off an upset in a best-of three match, but he's less likely to do so in the longer format. The same is true in other sports. In cricket, the better team is more likely to win a two-innings match than a Twenty20 game, and in football the league, played over 38 games, is a better measure of teams' true ability than the FA Cup.