Persia's response (attack with overwhelming force) seems perfectly predictable...were the leaders & citizens of Athens unclear on the forces at Darius' disposal, or have some reason to believe they would not be the focus of Persian wrath, or did they pledge their support in full knowledge of what they were inviting on themselves?
There's really three factors at play here:
Last point first since it's easy to just get out of the way. Athens and Euboea assisted the Ionian rebels for just one brief campaign, were soundly defeated, and withdrew from the war entirely. They only participated in the lightning raid on Sardis in 498 BCE and successfully razed the city in a surprise attack. By Herodotus' account, this was the first significant battle of the revolt and there were no Persian forces from outside of Lydia present. However, those local forces, presumably cavalry to account for the speed needed to catch up to the Greeks, caught the allied mainland-Ionian force outside of Ephesus and dealt a devastating defeat. Following the Battle of Ephesus, Herodotus says the Athenians refused to aid the rebels at all. So Athens was chased out of the revolt not by overwhelming force but by the display of any force at all.
At the outset of the Ionian Revolt, Aristagoras of Miletus went to mainland Greece to seek out allies. He started with Sparta because, according to Herodotus, they officially pledged to protect the Greeks in Asia from Persian hostility following the Persian conquest of Lydia (though they had never actually honored that commitment). Aristagoras brought a map of the known world engraved on a bronze tablet. In all likelihood this was the world map of Hecataeus, the Milesian chronicler, who was a major political figure in Miletus at the time. Of course, no copies survive but written descriptions based on Hecataeus' work show that he had a relatively accurate understanding of the Mediterranean, Egypt, and West Asia as far as the Persian palace capital at Susa.
In Herodotus' description of negotiations between Aristagoras and the Spartan king, Cleomenes, he at least makes it sound like the Milesian aristocracy understood the size of the western Persian Empire, but with only vague details about the population and the terrain. However, Herodotus makes it absolutely clear that the Spartans had no idea about any of it. In typical warfare between Greek city-states, the obvious plan was to target the enemy's capital, so Cleomenes wanted to know what it would take to attack Susa and was horrified to discover that Susa was more than 1400 miles away and refused to undergo such a campaign. The Spartans just had no concept of how far east the Persian Empire went in 499 BCE, and Susa was only really halfway through the Empire.
There's not much reason to think that the Athenians had more knowledge of West Asia than the Spartans, but when Aristagoras negotiated with them, he avoided the pitfalls he had made in Sparta and focused on conducting a war against Satrap Artaphernes and his capital at Sardis, limiting the scope of what he was talking about to a realistic goal and making the campaign sound more appealing. Athens was also, technically, at war with Persia before Aristagoras even arrived. When the Spartans were invading Attica to oust the Peisistratid tyrants in 510 BCE, Athenian envoys to Artaphernes submitted earth and water to in exchange for Persian support, officially submitting Athens to Persian rule. They envoys were lambasted for this when they got home and Athens disregarded their submission, but from the Persian perspective that just made Athens a subject state in rebellion.
So that is the backdrop for Athenian intervention in the Ionian Revolt, they did not have a full grasp on the scale of the Persian Empire and were already at odds with the Persians. Aristagoras further framed things as a local affair in western Anatolia, but kept emphasizing some of the same points he used in Sparta. One was the immense wealth of the Persian treasuries, which was true enough whether you frame it in terms of Sardis or Susa. The other main point played into Greek chauvinism. Herodotus puts this (probably made-up) quote in Aristagoras' mouth:
Now, therefore, we entreat you by the gods of Hellas to save your Ionian kinsmen from slavery. This is a thing which you can easily achieve, for the strangers are not valiant men while your valor in war is preeminent. As for their manner of fighting, they carry bows and short spears, and they go to battle with trousers on their legs and felt caps on their heads. Accordingly, they are easy to overcome. Furthermore, the inhabitants of that continent have more good things than all other men together, gold first but also silver, bronze, colored cloth, beasts of burden, and slaves. All this you can have to your heart's desire. (Histories 5.49.3-4)
Though they were not the only troops in a Greek army, the ancient Greeks did pride themselves on their heavy infantry, the hoplites. Aristagoras' description of Persian warriors emphasizes how they were exceedingly unGreek and had all the stereotypes of weak fighters in the Greek imagination: fighting at a distance, unprepared for close combat, constricting themselves with trousers, unprotected by helmets. To a certain degree, this was all true, if framed in a mocking way. The Persians themselves did emphasize archery in their armies, carry shorter spears than the Greek doru, and the cavalry and poorer infantry did fight without helmets in the early 5th Century. However, Aristagoras intentionally neglected to mention that they also recruited heavy infantry from loyalist Greek and Carian cities, Lydia, Egypt, Mesopotamia, and Phoenicia. This presentation may have played a role in Athens abandoning the cause early on.
Based on the one allied Ionian-Athenian-Euobean action attacking Sardis, he may have hoped it wouldn't be relevant. A blitz-like attack on the provincial capital as the opening salvo is pretty daring, and Aristagoras and the Ionians may have been hoping it was enough for a swift victory before major reinforcements arrived.
That brings me to point 2. Darius dispatching three generals in command of full armies in addition to Artaphernes' local garrisons is almost unique in the history of Greek invasions of Persian territory. Aside from the Spartan invasion of Anatolia in the early 4th Century BCE, there are no historical reports of major Persian reinforcements coming to aid the satraps of western Anatolia in their wars against the mainland Greeks. The conquests of the Delian League, the Ionian theater of the Peloponnesian War, and the 4th Century wars after the Spartan king, Agesilaus, withdrew were all conducted by the local satraps themselves with apparently minimal royal aid. Even the initial Persian conquest of Ionia following the Lydian revolt of the 540s BCE was conducted by single generals sent by Cyrus the Great while the king himself focused on campaigns in the east. Even other campaigns of conquest in the Aegean, such as the then-recent annexation of Thrace and Macedon, had been conducted by smaller forces under single commanders.
Nothing about Persian policy before or after, from the Greek point of view, provides significant precedent for the kind of response Darius the Great sent in 497 BCE. To be sure, the Persians dealt with rebels harshly, but overwhelming force was rarely the name of the game. However, the Greek authors from Herodotus on down are almost entirely ignorant of one of Darius' formative experiences, which may have colored the response in the 490s. When Darius the Great came to power through a coup in 522, the Persian Empire shattered. In his Behistun Inscription, Darius records 9 rebel kings and implies at least one more, Egyptian records add an 11th, and Herodotus insinuates an 12th in the form of Artaphernes' predecessor.
I feel comfortable describing the revolts/civil war of the late 520s as a formative experience for Darius because, unlike his successors, he references this conflict in numerous inscriptions. From all the later Persian kings, there is just one additional example of an inscription referencing a rebellion or war, and even that one does not emphasize the defeat of the rebellion itself. It was important to Darius to emphasize his victory over rebels in a way not reflected by other kings.
Herodotus also records how Darius had Aryandes, his Satrap in Egypt, removed from office on suspicions of rebellion, had one of his co-conspirators in the coup executed on similar suspicions, and took Aristagoras' predecessor into exile in Persia on suspicion that he might try to revolt. So Darius was clearly on the lookout. It's not surprising that the Ionian Revolt prompted a massive response from his perspective, but it may have been more unexpected for the Greeks.