Having a single example of a good short player doesn't mean size doesn't matter. There may be a positive correlation between size and "skill", and Messi is one of the best despite his size disadvantage.
Germany: Philipp Lahm 5'7" and Mario Gotze 5'9" Belgium: Eden Hazard 5'8" Italy: Andrea Pirlo 5'9.5" Netherlands: Wesley Sneijder 5'7" Spain: Xavi and Iniesta 5'7"
historically the best players have been on the shorter side. Maradona was 5'5'', Pele 5'8''. One of the greatest parts of soccer is that it doesn't immediately disqualify 70%+ of the potential talent pool based on the importance of a single attribute, like height in basketball.