The Battle of Marathon was pivotal primarily due to it showing that the Persian forces could be defeated. Within the Greco-Persian Wars, this battle marked the culmination of Persia's first invasion of Greece, under the rule of Darius I (the Great).

There's a bit of tension that leads up to this point. Cyrus the Great conquered Ionia in mid-4th century BCE, which was inhabited by Greeks. The territory was placed under the rule of Persian-appointed governors, but rebellion was always on the periphery. After a debacle that lead Persian-appointed tyrant Aristagoras of Miletus to believe he was going to be stripped of his power, Aristagoras beat Persia to the punch by leading all of Hellenic Asia Minor into rebellion, known as the Ionian Revolt (499-493 BCE).

The year 498 BCE is crucial, as Athens and Eretreia provided military aid to the rebels, leading to the capturing and burning of Persian regional capital Sardis. Darius vowed revenge on the Athenians and Eretrians for their participation in the sacking of Sardis, allegedly having a slave whisper in his ear before every meal "Master, remember the Athenians". The Ionian Revolt was a effectively a stalemate for the next few years, until Persian forces squashed it, ending it in 493.

This is where Marathon begins to come into the picture. Persia effectively stamped out any further thought of revolution in Ionia, and Persian general Mardonious conquered Thrace and Macedonia on a campaign to bring mainland Greece under Persian rule. A second naval force was sent to Greece to exact revenge on Athens and Eretria, the latter city was besieged, captured, and subsequently razed in 490. This force began to make its way towards Athens, but they would meet the Athenian and Plataean force at the plains of Marathon. Sparta, notably absent, didn't provide aid in the urgent manner that was necessary.

The coalition of Athenians and Plataeans was comparatively weaker than their Persian counterparts, outnumbered probably 2 to 1, however Athenian general Miltiades used cunning strategy to achieve victory. By reinforcing his flanks and drastically thinning out the center of his forces, they looked as if they were attempting a suicide march. Persian forces charged directly at the weak center, and were then surrouned as the reinforced flanks came in from the sides and engulfed them, routing the army.

However, a Persian fleet - seeing Athens' military out of the city - immediately sailed towards Athens to attack it. I can't remember the exact quote, but Miltiades told the soldiers to haul ass back to Athens. They arrived just in time to prevent a Persian landing, and the fleet returned to Asia, thus ending the first invasion of Greece.

Darius' son Xerxes would return 10 years later, and we know of that thanks to Frank Miller. However, the heroics at the battle of Thermopylae were preceded by a smaller force routing the thus far unbeatable Persians with time left over to get back and protect their city. The Athenian/Plataean victory quite literally saved Athens from a fate similar to Eretria's. Not that Athens wouldn't get sacked in due time, but it was a turning point in 490 because it showed that they were capable of defending Greece from Persian invasion.

Source: Richard Billows, Marathon: The Battle that Changed Western Civilization; he was my professor in undergrad at Columbia University, I'm currently in their ancient history doctoral program, and the battle of marathon is a personal favorite.