Ruins are remains of structures built by the Old Ones. They come in two types, buildings and bunkers.
A millennium before the events of Horizon Zero Dawn, the Old Ones had become quite advanced in the construction of machines. By the 2060's, they were used to for transportation and entertainment purposes (i.e. Focus devices and advanced aircraft and land vehicles.) However, the environmental situation was at an all time low. These conditions led to many manufacturing corporations like Faro Automated Services to construct armed machines for peacekeeping purposes. Things got worse when the Faro Plague began. Cities were used to either as recruiting stations or as collateral damage during Operation: Enduring Victory. At the same time, bunkers were installed to help make GAIA installations or for the military.
Once the Plague wiped out all life on the planet, the cities, now ruins, went unused and began to rust away. When the new human population left the Cradle facilities, they found the cities unnerving or foreboding, not trustworthy, and began to build new settlements, leaving the structures to decay away.