Being able to understand where your data is located in a computer and knowing how to manipulate them makes a lot of subsequent data management easier. For one, a file system is independent of any given piece of software. You don't need to rely on your word processing program knowing where your documents are, you can just tell it where your document is. You don't need to wrangle with sending a picture from your Photos program to your email program, you can tell your Photos program where to save the picture and you can just tell your email program where your picture is.
And did I say picture? Is it a JPEG? PNG? GIF? An abstraction of the file system won't tell me, but if I go look in the file system I can immediately tell what the picture is, and where it is too.
And like I just alluded to, you get to decide where the files reside too. Your Photos program might stuff all 6000 of your pictures under "C:\Program Files\VendorMcVendorface\Photos\userdata", and sure, that works, but that's nonsense. You could sort everything exactly how you want it where you want it. "C:\Photos\2006\Yosemite" for just all the pictures you took on a trip to Yosemite National Park in 2006, for example.
Admittedly, it's a feat that file systems have been successfully abstracted away for Joe Average, but not knowing how to navigate and use file systems is going to bite you in your arse when something inevitably comes around demanding you do it.
Understanding file systems is one of those bits of knowledge and wisdom in life you can do without, until you can't. And by then, you don't have time to call for a time out and get a crash course on it.
If you’re someone who likes working with the filesystem directly, why? Seriously why? It really does seem like anything would be better.
Even for code, wouldn’t you rather things like Python modules or packages be first class objects? No more sys.path nonsense, no more namespacing, just your whole venv in a single trivially relocatable file.