Something to realise when starting with Linux is that everything is a ‘file’. Sockets, processes, input, output etc. That’s very different from Windows and part of why scripting on Linux is so powerful. You can interact with anything.
So some directories are filled with things that aren’t necessarily files but look like it. Someone else posted a whole list, just realise that under those directories/paths shouldn’t be messed with unless you know what it’s for.
Generally when you’re getting used to Linux, /home/$user (aka ~) is where you put personal things. The rest is managed by OS and applications, don’t worry about it.
Edit: spelling
Something like that indeed.
Every active network connection, every process, every piece of hardware and others are in your file system.
Then there’s also the possibility for linking to a file and links take up no space, but can show up like files.
You can use a command like ‘stat’ to get more information about a file (or directory).