1. Many users find recursive data structures like trees to be confusing. Recursion is the place where a lot of students fall off the train when learning programming. Trees are fundamental to file systems and explorers, but they aren't intuitive to a lot of people. That's why every app now starts with a screen that highlights recent documents and search.
2. Developers hate files because files suck. They're just flat arrays of bytes. You have to define file formats and that is really hard work many programmers have never done. Databases are where it's at but RDBMS tech never standardised file formats, hence the appeal of SQLite's "use an rdbms as your file format" elevator pitch. Apple/NeXT tried to partly fix this with the concept of bundles, but our industry never standardised a way to transmit directories that works better than PKZIP so bundles hardly work and Apple had to give up on them in most cases. None of the protocols we use understand how to move directories around.