Persia certainly had no motive for destroying the economies of the peoples in its empire.
Naturally, it expected the ruling groups or individuals to guarantee payment of tribute and generally deferential behaviour, but then the Athenian and Spartan empires expected the same of their dependents.
Political dislike of satrapal control is also implied by the concessions made after the revolt ended in 494: the Persians Artaphernes and Mardonius granted a degree of autonomy by instituting a system of intercity arbitration; they abstained from financial reprisals and from demanding indemnities and merely exacted former levels of tribute, but after a more precise survey; and above all, Herodotus says, they “put down all the despots throughout Ionia, and in lieu of them established democracies.” The meaning and even the truth of this last concession are alike disputed.
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A simple economic explanation, such as used to be fashionable, is no longer acceptable.
Perhaps one should look instead for military causes: Ionians disliked the military service to which they were then compelled (they did not even care much for the naval training they had to undergo, in a better cause, before Lade).
The situation for the far more numerous smaller states of mainland Greece was different inasmuch as a distinctive policy of their own toward Persia or anybody else was hardly an option for most of the time.
However, Eretria, by now a third-class power, had its own unsuccessful “war” with Persia in 490, and some very small cities and islands were proud to record on the “Serpent Column” (the victory dedication to Apollo at Delphi) their participation on the Greek side in the great war of 480–479.
For instance, one reads at the very end of Herodotus’ history (concerning the year 479) of a temple on Asian soil to Demeter of Eleusis that had been brought over by the Ionians from Attica in the early Dark Age and was still going strong, presumably without a break.
So the improvements introduced after 494 consisted in the increase, not in the outright introduction, of local self-determination within the satrapal framework.
The reasons for Herodotus’ hostility have partly to do with anti-Milesian sentiment specifically in fellow-Ionian Samos, where he gathered some of his material (the Samians seem to have tried to represent the failure as due to the incompetence and ambitions of Milesian individuals), and partly with the generally Ionian character of the revolt (Herodotus’ home town of Halicarnassus was partly Dorian, partly Carian).
In addition, he was influenced by defeatist mainland Greek sources, particularly by Athenian informants who resented Athens’ unsuccessful involvement on the rebel side.
The puzzle is to explain why the revolt happened when it did, after nearly half a century of rule by the Achaemenid Persian kings (that is, since 546 when Cyrus the Great conquered them; his main successors were Cambyses [530–522], Darius I [522–486], Xerxes I [486–465], Artaxerxes I [465–424], and Darius II [423–404]).