Other have already made some good points, the difficulty or resource poverty to repair damaged buildings, and cultural changes that meant some buildings suddenly become undesirable.

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At which point they have often been converted into a five fingered discount quarry.

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They have been very, very vulnerable to resource looting. Sometimes for ordinary buildings, sometimes for other monuments and other religious buildings.

Often new churches were built on the same site as the former temples, renovating or reusing older parts of the structures.

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Some were also used as churches without much adaptation, like the Pantheon, which is still to this day an active church. Though a pope did mug it during the 17th century and absconded with a lot of bronze and marble to build the Barberini Palace.

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In the eastern part of the roman empire (byzantine empire) many temples and shrines were demolished by decree and reused to build new churches.

A church in Hagios Kosmas used stones and columns from a shrine to Aphrodite. As far as researchers can tell just about every bit of that shrine is gone and more or less recycled into various structures, some which are also long gone by now.

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Quite a bit of the Colosseum that had been damaged by earthquakes and then some was carted off to build medieval and renaissance Rome, until a pope in 1744 put his slipper down and banned the practice as well as declaring it a protected site that could not be demolished. Parts of it is in Barberini Palace, Piazza Venezia and St. Peter's.

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You can find stones from a building dedicated to Ramses II (Died 1213 BC) used miles and miles away from it's original place to build the gateway for Shoshenq III (Died 798 BC).

For when you still wants that glorious builder prestige but haven't quite got the same budget. In that case Ramses was from a very different family and time, but Shoseng III wasn't averse to taking from his direct ancestors either.

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Recycled sarcophaguses too. Some previous occupants might have been dumped who knows where, and some found themselves reinterred in less fancy environments with new roommates.

And some dispensed with relocating entirely and just cleared out the previous incumbent, relabeled stuff and moved in after death.

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If people ever wonder why we don't know where more pharaohs, their relatives and other dignitaries mummies are and who's whom, this is also one of the reasons. You can't even trust these people to stay in their own graves.