Actually, people probably did scavenge from the villa. The article doesn't go into much detail (and we probably don't know many details yet) but there's no reason to assume that nothing was stolen from the villa before people moved out of the area.

Note that this villa would have been enormous, larger than many modern houses. So it would be quite easy for a thief to miss something.

Also note that some of the most valuable things (like the mosaics) would have been very difficult to remove and probably would not be worth the effort for most people.

The ground literally rises by a certain amount (very small amounts of course) every year. This is just through silt and dirt and dust being blown around by the weather so abandoned areas will gradually get covered if they're not maintained. This is basically the law of entropy, order will turn to chaos (unless maintained).

Also worth noting, as already pointed out, its highly likely that plenty of looting took place in abandoned places. Walls would have been pulled down to reuse the brick and stone for other houses and so on which is why its typically only foundations and ground floors that get preserved. Its not like there's a full 2 story mansion preserved in tact under the ground. The only time this happens is, well, Pompei.

In addition to what others have said, sites may be abandoned after being sacked or "destroyed". That destruction may make the site uninhabitable or simply not useful to the people of the time yet preserve things for later archaeologists. As an example, the city of Mari in the Ancient Near East was conquered and burned by Hammurabi. This had the unintended side effect of preserving many clay tablets and administrative records that began to be excavated after the city's rediscovery in 1933.