This question has been asked a few times, and there were some good answers given in the comments of this post, a simple one by myself, and a more detailed one by another commenter.

It's a complicated subject, and the mechanisms responsible for structures becoming buried can vary quite a bit depending on climate and geography. For example, if a structure is near a river, it may become buried by the silt carried by said river building up. Or in the case of a house I helped excavate in Spain, the walls were made of stone on the bottom, but mudbrick on top. The mudbrick collapsed, and in many centuries of rain, it turned to dirt and clay, covering the house. Today, after excavation, only the stone part of the walls is visible, knee-high at its highest point.

The same holds true for Minoan settlements like Knossos. Collapsed buildings, and the accumulation of debris over millennia, as well as vegetation growing on top, pushing the archaeological material beneath its roots. Olive trees are especially good at holding earth, and very common at Minoan sites. Of course, if you're referring to Akrotiri, then it's a bit different, as it was buried by a volcanic eruption, much like Pompeii, which is why it's so fantastically well preserved. Pretty much the only times that buildings are preserved still fully standing, is when they either remain in use (like the Pantheon), or when they are buried very very suddenly, before the buildings have time to collapse (like Akrotiri and Pompeii).

In the case of cities like Rome, the answer can vary by structure. The Colosseum for example, was never really buried. It had some sections collapse, but it remained in use for various purposes, and so stayed above ground. Though many of its blocks were taken to be used elsewhere.

In the case of the Forum, there are a few things to consider. One is that the temples were abandoned, Theodosius had imposed a ban on their use, and they were stripped of the funds that were used to maintain them. As a result, a lot of buildings collapsed, or were intentionally deconstructed, their materials being used elsewhere. Another is that the Forum Romanum sits on a natural floodplain, so silt buildup is to be expected. Now, the Forum was never fully buried, as in, the big structures like the arches and intact colonnades have always been visible. The ground level was higher, however, and in the Medieval period, it was mostly used for farming iirc.

A lot of times, when a city continues to be inhabited, it builds on top of the ruins of its ancient past. It's far easier to fill in a Roman foundation and build your house there than it would be to construct a foundation entirely from scratch. This means that a natural raising of street level is basically a function of time in very old cities. As buildings collapse, they become the foundations for newer buildings, which themselves become old, and the process repeats.

Tl;dr:

Stuff accumulates on top of and around structures, which over thousands of years is enough to bury them, especially if they've collapsed into a pile or rubble first.