My experience has been the complete opposite. I find the file system, far, far more intuitive than all the ad-hoc ways various applications attempt to manage my "content" for me. With these apps that abstract away the filesystem, you can never really be sure you have the right mental model of your data. The way apps like iTunes store your data is just so opaque.
Indeed, iTunes is the perfect example of this problem. I can't count how many people have come to me utterly confused about how syncing between your hard drive, iOS, the iTunes store, and iCloud works. They can't understand it because Apple imposes an ever-shifting system of abstractions onto your music storage. You don't have music files anymore. You have songs stored in certain libraries, and those libraries can be "synced" with each other in ways that often result in strange error messages and loss of data.
Imagine instead that things worked like the old days: You just have MP3 files, and you can put them in folders. The iPhone, when connected to the computer, can be accessed like any other filesystem. You move files in and out of a folder called iPhone/Music. In this alternate reality, you'd understand exactly what you're doing. You wouldn't have to guess at how "syncing" is going to change the state of your data.