Many of them were! Obviously here are some ruins that were completely abandoned and stand alone in that Romantic way we like to picture them, and the ruins that are left alone and untouched will naturally be rather more complete than those that were taken apart, repurposed, added to, and otherwise changed to fit changed needs, but the reason they are untouched is because they were alone as people just stopped living there. So, for example, if you go to Termessos in southern Turkey (and you should if you can) you will walk along evocative ruins that seem intact and abandoned, and that is because humans stopped living there.

To take a contrary example, consider the Acropolis of Athens, a city that has certainly had its ups and downs over the years but has maintained some sort of habitation. Right now there is an ongoing project to "un-explode" the Parthenon by meticulously placing each stone back in the place it was, and the end result will be a highly exact copy of an ancient structure that is completely unrepresentative of its history. The Acropolis has been systematically cleared of the mosque, the Church, Frankish fortification, Ottoman barracks, really anything that violates the image of a pure, gleaming white structure rising out of the bedrock. It is a deeply modernist project that has very little to do with how the space was ever actually used, and it is emblematic of the way that our image of the "untouched ruins" is basically a projection, not a reality.

The use and reuse of ancient structures is far too big of a topic for any one book, but Mary Beard's The Parthenon is a good detailing of that one specific case. You also might look at Mario Erasmo's Strolling Through Rome for just how much of the ancient city has been incorporated into the modern one.