The Parthenon's current state can be attributed to its use as a gunpowder magazine by the Ottomans. The magazine detonated when hit by Venetian mortar fire in 1687. Here's the aftermath as described by archaeologist Kornilia Chatziaslani:

As a result of the explosion, three of the sanctuary’s four walls nearly collapsed and three-fifths of the sculptures from the frieze fell. Nothing of the roof apparently remained in place. Six columns from the south side fell, eight from the north, as well as whatever remained from eastern porch, except for one column. The columns brought down with them the enormous marble architraves, triglyphs and metopes. The entire building suffered a fearsome shock. The blast and the blowing up of the building created indescribable panic. Three hundred Turks were killed by the marble that was launched in all directions. The fire spread to surrounding homes, and, since there was not enough water, became extended ever further. The entire night of September 26 (towards the 27th) as well as the entire next day, the Acropolis burned.

Ditto to serverofjustice's post. Additionally, Athens did not remain stagnant during the Roman Empire. For example, the beautiful Odeon of Herodes Atticus was built during the second century CE. A cult complex was built by the brother of P. Clodius Pulcher to facilitate the Eleusinian Msyteries in the first century BCE. Perhaps most importantly, the emperor Hadrian is considered to be a new founder of Athens. He built the arch of Hadrian, the Library of Hadrian, and a number of other buildings.

Just to add on to /u/Enrico_Dandolo's comment about Hadrian, I wrote a paper this past semester on Hadrian's construction projects in Athens. He had a great respect and appreciation for Athenian history and its place of important in pre-Roman times, and went about restoring the city to its former glory.

The Arch of Hadrian really highlights this fact. It was built by the Athenians to honor Hadrian's contributions. On the side of the arch facing you as you approach the Acropolis, it reads, "This is the city of Theseus" (Theseus being the traditional founder of the city of Athens). On the reverse side, visible to any heading out into the city with the Acropolis at their back, it reads, "This is the city of Hadrian, not of Theseus." Some scholars initially took this to mean that there was a literal subdivision of the city into the "old city" around the Acropolis and a "new city" built up by Hadrian surrounding it. However, the most prevalent interpretation today of the inscription, and of Hadrian's relationship with Athens, is that he wished to portray himself as the second founder of the city, and that the new, refurbished city of Athens belonged to him, not to a mythological figure.