One of the reasons is high resilience, practically state of the art as far as writing to a single storage device allows. You're less likely to end up with corrupted files with sqlite. This is much more difficult to get right when manipulating files yourself than you might think.
For your consideration (I'll add that I used to think similarly as you, and I still wouldn't use sqlite for everything, but it's shockingly effective):
For your consideration (I'll add that I used to think similarly as you, and I still wouldn't use sqlite for everything, but it's shockingly effective):
https://www.sqlite.org/transactional.html
https://www.sqlite.org/fasterthanfs.html
https://www.sqlite.org/atomiccommit.html
https://www.sqlite.org/aff_short.html
https://www.sqlite.org/testing.html
https://danluu.com/file-consistency/