Actually it is somewhat of a pattern that the greatest players of all time have been a little short.
Again it's mostly to do with agility and such things which smaller people do generally have more of.
Actually, goalkeepers are generally pretty tall.
Pele, Maradona and Messi (I assume those are the "greatest players" you're talking about) are/were all extremely good, but there are other positions in a football team. None of them would make particularly good defenders or goalkeppers, for example. Labelling someone the "best" is, in my opinion, harder than a lot of people make it out to be, because the players are valuable to their team in different ways depending on which position they play on.
All those best player awards and titles are extremely biased, because they almost always go to offensive players, since their performance is directly noticable. A lot of what for example a defender does during a match passes by unnoticed, because they're often trying to position themselves in a way that avoids a dangerous situation entirely, which often makes it look like they didn't do anything at all.
To put the above into an example, I'd argue that Xavi is a much more important player for Barcelona than Messi, but Messi ends up winning all the awards because he's fast, technical and scores all the goals.
If you want to be one of those speedy, super technical players (Messi, Maradona), then yes, not being tall might give you a small advantage, but other than that, it doesn't really make a difference (in fact, it's a bit of a
disadvantage if you want to be a goalkeeper, or if you play in one of the more physical leagues, such as the English or Scottish ones).