What caused the subjects of the Persian empire to rebel?

Aristagoras, the Greek tyrant appointed to control Miletus, persuaded the Persian provincial governor into a joint attempt to take Naxos. When this failed, Aristagoras knew he was set for retribution, and conned the other Greek cities of Asia Minor into rebelling against Persian rule, leading to 50 years of warfare between the Persian Empire and the Greek city-states of the Eastern Mediterranean.
The Greek city-states were conned into rebellion by Aristagoras, a Greek who the Persians had appointed as tyrant of Miletus. He had talked the Persian governor into supporting a takeover of Naxos; it failed and he knew that punishment was coming to him, and organised the revolt by the already restive Greek city-states to protect himself, known as the Ionian Revolt beginning in 499 BCE.