This is a big question with multiple answers. I am a history undergrad with a focus on ancient architecture. I'll share a little bit from what I've learned in my classes.

1. Some of these historic sites get totally buried. With the volatile geology of places like Greece the earthquakes that they have and the degree of erosion that they experience off of their mountains and hillsides, huge buildings can be entirely swallowed up. For example, the Athenian Agora was almost entirely buried until about 1930. The only structure that was still visible was the a single temple ( I'll come back to that in a minute). The rest of it had been literally buried from erosion. On top of that burial there were people that had constructed homes and they were compensated and removed by the Athenian and Greek governments in the '30s that way the American schools of architecture could come and excavate the original agora.

2. They often get repurposed. The structures that wind up standing, like the Hephesteon in the Athenian Agora, do so because they were maintained or taken over by church usually. These are incredible structures that were built to impress and intimidate when they were constructed and they still serve that purpose thousands of years later. The Greek Orthodox Church used it as a cathedral for an extended period of time, I don't actually know how long, but it's the Greek government has gotten involved in the archaeological societies have become more involved It has been restored.

Another way of repurposing an ancient building is to go and take stone out of an original building and use it for whatever it is that you are building. This is really common at archaeological sites that are near small towns or cities where gaining resources might be difficult. If you're a farmer building a stone wall and you have a theater nearby where nobody ever goes, it seems practical to go and just take one of the stones that are there and use them in your wall. This is really common throughout the ancient world and people recover random pieces of text and stole (stones that have engravings on them) all the time in really weird places. What's cool is that if it's done carefully then it can sometimes be one of the best ways to preserve a stole.

3. Resources are not always available. And some other redditors have pointed out, when a major powerful government like the Athenian League or the Roman Empire collapses the resources become less available because they take colonial holdings in order to keep in order. Without those colonial holdings it gets much more difficult. There's also a time and focus issue, It takes a long time to maintain and reconstruct some of these buildings and if no one really cares to do it then they just fall into disrepair. Especially considering the ubiquity of limestone, and how limestone reacts with acid rain, sometimes this can happen really quickly.

4. Some of the disrepair is intentional. Some of these buildings fell apart a long time ago through events like earthquakes for example. That earthquake destroying the building imparts its own history into that building. And if an archaeological team goes out and only puts up four or five columns it gives enough, visually, to reconstruct the rest of the building on paper. And really that is what is the intent. They leave them knocked down because to restore them exactly as they used to be, would be incredibly expensive and it kind of takes away from some of that history.

I don't know if that was e l i5 enough, but I really care about it and it's hard to talk about it in other terms.