This is a tricky problem. Most of the sites worth seeing in Athens, require you to cross or go very near the protest centers. For someone on a 2 week vacation or less, I don’t recommend staying in Athens more than 2 nights anyway, so personally I’d recommend bypassing Athens and going straight to the Islands or other mainland cities.

Here are some other rules of thumb if you want to stay near or in Athens:

-Stay away from Syntagma Square.
-Stay along the Athens coastal cities like Pireaus or Vouliagmeni
-Greece is generally a destination for the more adventurous traveler, so make sure it's the destination for you.