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The clearest reference (that I can find) to a positive view on height is in Aristotle's Nicomachean Ethics (Book 4, Chapter 4):
The man who estimates himself lowly, and at the same time justly, is modest; but not Great-minded, since this latter quality implies greatness, just as beauty implies a large bodily conformation while small people are neat and well made but not beautiful.
However, Aristotle (in On the Generation of Animals, Book IV) also observes that
for each species, there is a certain range within which size varies: so a human as large as an elephant would not be beautiful.
Source: M. Heath, 'Unity, Wholeness, and Proportion'. Chapter 25 in Pierre Destrée and Penelope Murray (eds.), 'A companion to ancient aesthetics' (2015)
Further, Plato (and others) also emphasised the importance of proportion of the parts of the body. Thus, tall people being viewed positively was subject to both proportion and the perceived norms of the size of humans. Also, although physical beauty was of great importance to the ancient Greeks, so were non-physical factors such as family and character - note also kalokagathos. Athletic prowess was also highly valued in society and this, of course, did not depend on height in many cases.
A note on Herakles' height
Ancient authors' descriptions of Herakles' supposed stature varied. The poet Pindar (d. 438 BC) described him as short. However, the writer Herodorus (active in c. 400 BC), who wrote a monograph on Herakles (among other mythical figures) of which only fragments survive, described the hero as being unusually tall (as did later Roman writers). Also, according to Aulus Gellius' work Noctes Atticae, Pythagoras (died circa 495 BC) attempted to calculate Herakles' height based on the hero's estimated foot size and arrived at the conclusion that he was "much taller than other men".
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At least some of the classical Greek authors indicate a belief that Heroes of old were much taller, larger, and stronger than the men of their own times. I should say that this may or may not tell us anything in particular about how they thought about height in men or in women in their own times. But there are a couple of weird episodes recorded by Classical historians of that seem to indicate a belief, among Classical-era Greeks, that the Heroes of old were much larger and much taller than mortals today.
@LarsBosteen has some interesting notes above about differing traditions about the height of Herakles. I would add that there are at least two weird stories in which Greeks in the Archaic or Classical era claimed to have discovered the bones of a long-dead Hero, and took them back to their own city (in order to care for them and to receive power from caring for them).
The Spartans claim to discover the Bones of Orestes. Herodotus I.67-68 tells a weird story about the war between Sparta and Tegea during the reign of Anaxandridas II and Ariston (around 560 BCE). The Spartans had been losing the war when they sent a question to the Oracle at Delphi, which revealed to them that they needed to find the tomb of Orestes son of Agamemnon, recover his bones, and bring them back to be interred in Sparta. Herodotus says they discovered the bones in the courtyard of a blacksmith's shop in Tegea, then used trickery to recover the bones for themselves:
Hdt. I.68 [...] It was Lichas, one of these men, who found the tomb in Tegea by a combination of luck and skill. At that time there was free access to Tegea, so he went into a blacksmith's shop and watched iron being forged, standing there in amazement at what he saw done. [2] The smith perceived that he was amazed, so he stopped what he was doing and said, "My Laconian guest, if you had seen what I saw, then you would really be amazed, since you marvel so at ironworking. [3] I wanted to dig a well in the courtyard here, and in my digging I hit upon a coffin twelve feet long. [σορῷ ἑπταπήχεϊ, sorho heptapekhei; "a seven-cubit coffin," really more like 10.5 ft —AS] I could not believe that there had ever been men taller [μέζονας, medzonas, from megas, big, great, high or tall —AS] than now, so I opened it and saw that the corpse was just as long as the coffin. [τὸν νεκρὸν μήκεϊ ἴσον ἐόντα τῇ σορῷ, ton nekron mekei ison eonta te sorho, "the corpse being equal in length to the coffin" —AS] I measured it and then reburied it." So the smith told what he had seen, and Lichas thought about what was said and reckoned that this was Orestes, according to the oracle. [4] In the smith's two bellows he found the winds, hammer and anvil were blow upon blow, and the forging of iron was woe upon woe, since he figured that iron was discovered as an evil for the human race. [5] After reasoning this out, he went back to Sparta and told the Lacedaemonians everything. They made a pretence of bringing a charge against him and banishing him. Coming to Tegea, he explained his misfortune to the smith and tried to rent the courtyard, but the smith did not want to lease it. [6] Finally he persuaded him and set up residence there. He dug up the grave and collected the bones, then hurried off to Sparta with them. Ever since then the Spartans were far superior to the Tegeans whenever they met each other in battle. [...]
Herodotus would have written this story down sometime around 430 BCE.
The Athenians claim to discover the Bones of Theseus. Plutarch, Life of Theseus 36.1-2 tells a similar story -- structurally similar, and similarly weird -- about the Athenian general Cimon, who had led the conquest of the island of Skyros and planted an Athenian settlement on it. He then got an oracular message and supposedly discovered a huge coffin on the island containing the giant bones of Theseus, King of Athens, which he dug up and brought to be interred at a shrine in Athens; this continued to be a devotional center in Athens for centuries afterwards. (The supposed discovery would have taken place sometime in the 470s BCE; see this note from A. J. Podlecki on dating the event.)
Plut. Thes. 36.1 And after the Median wars, in the Archonship of Phaedo, when the Athenians were consulting the oracle at Delphi, they were told by the Pythian priestess to take up the bones of Theseus, give them honorable burial at Athens, and guard them there. But it was difficult to find the grave and take up the bones, because of the inhospitable and savage nature of the Dolopians, who then inhabited the island. However, Cimon took the island, as I have related in his Life, and being ambitious to discover the grave of Theseus, saw an eagle in a place where there was the semblance of a mound, pecking, as they say, and tearing up the ground with his talons. By some divine ordering he comprehended the meaning of this and dug there, [2] and there was found a coffin of a man of extraordinary size, [θήκη ... μεγάλου σώματος, theke megalou somatos, "a coffin with a huge body" —AS] a bronze spear lying by its side, and a sword. When these relics were brought home on his trireme by Cimon, the Athenians were delighted, and received them with splendid processions and sacrifices, as though Theseus himself were returning to his city. And now he lies buried in the heart of the city, near the present gymnasium, and his tomb is a sanctuary and place of refuge for runaway slaves and all men of low estate who are afraid of men in power, since Theseus was a champion and helper of such during his life, and graciously received the supplications of the poor and needy.
Plutarch would have written this story down sometime in the early 100s-110s CE.
The view that ancient heroes were far larger might also have connected with the idea that you see in a lot of epic poetry that they were far stronger than men are today; for example, in the Iliad book 5, when Diomedes the son of Tydeus confronts Aeneas over the body of Pandarus:
Aeneas vaulted down with his shield and spear
Afraid that the Greeks might drag the body away
He straddled it like a lion sure of its strength,
Spear straight out, crouched behind his shield's disk,
Only too glad to kill whatever stood up to him,
His mouth open in a battle-howl. / But Tydeus' son
Levered up in one hand a slab of stone
Much too large for two men to lift—
As men are now—lifted it and smashed it Into Aeneas' hip...[Hom. Il. Book 5, trans. Lombardo]
I should say that I find this stuff really interesting, but it is not much of a direct answer to your question; though I hope it may offer some suggestive information toward an answer. Sometimes the things that people associate with their old-timey heroes and founding figures directly translate into finding those things admirable, or putting "a social premium" on them, when found in modern-day people as well. (For example, many people in medieval England thought of Sir Galahad as pious and chaste; and this partly reflects the idea that piety and chastity were admirable things in people of their own times.) But this isn't necessarily so. (The heroes in the Persian Shahnameh are all pagans, although the work and its author are Muslim; in many societies, it's common to think that old-timey heroes were rowdy or exceptionally violent in ways that might have been appropriate to the time, but which would be dangerous or evil in the modern world.) In any case, even if the view of heroes as exceptionally large does reflect a social premium on height among their contemporaries, tales like these tell us what some people thought, but not others. The views of Greek philosophers were often different from the views expressed in epic literature or in popular veneration and religious devotion; etc., etc., etc.