The ruins that we see today often didn't stand there as ruins for 2000 years. For example, the most iconic ruin of Athens, the Parthenon temple, continued to be used, first as a Christian church, then as a mosque, for centuries (making some small alterations to it like adding a minaret). No need to tear down a perfectly good building if you can still use it.

It only became a ruin after being damaged in a war, and for the next 150 years, the Ottomans couldn't be bothered to either rebuild it nor to tear it down. Both would be a lot of work, and they didn't need the space that bad, so they just used the rubble to build a smaller mosque inside the ruins and call it a day.

Then, Greece became an independent nation, and the ruins of Ancient Greece were of huge importance to their national identity, so they removed the mosque and everything else that had been added after antiquity, and made an effort to preserve what was left of the ancient temple. What we see today is the result of that effort.

Similar stories exist for nearly all ancient ruins in European cities - they continued to be used and were integrated into newer buildings for centuries, and then beginning in the 19th century people started to remove the newer buildings, uncovering what was left of the ancient buildings, and preserving these leftovers (or sometimes attempting to reconstruct them).