There isn't one single explanation. Every case is slightly different. Most, however, were buried during construction of newer structures. Street level tends to rise over the centuries in continually-occupied places, as old buildings are built upon. In Rome, at the Basilica of San Clemente, you start at street level in the church built about 1100 CE, then you can go downstairs about 10 meters to find yourself in the 4th century CE church beneath it, and then go down still further into a series of Roman rooms. Each successive layer was filled in and built upon as the centuries past. For mosaics, it was often too expensive to attempt to move them and reinstall them elsewhere. Many were just buried to create a nice level space for the next building, and forgotten about. Think about old wallpaper in houses today, or nice hardwood floors beneath carpets. Nero's famous Golden House was deliberately buried to make substructures for new, post-Neronian construction on top of it. The immaculate mosaics, wall paintings, and even statuary were just left to be entombed in filler rubble and would sleep there for nearly two millennia, waiting to be rediscovered by the artist-adventurers of the Roman early Renaissance.

Now in other cases, the building which housed the mosaic collapsed due to fire or earthquake or whatever. The mosaics and everything else were covered, and over the decades and centuries, the contents are forgotten. A good example is the discovery of the magnificent Bellerophon mosaic in Berkshire in recent memory. It was an element in a nice Romano-British aristocrat's villa, which probably was either destroyed or fell to ruin, thereby burying the mosaic and preserving it for nearly two thousand years.