My biggest thing when switching to Linux was understanding why I didn't have permission to alter half of my file structure. I was trying to take ownership of my /usr directory as a user and had to have multiple people explain why that was a bad idea (and why simply making any changes as a super user via terminal was more than adequate for the results I wanted).
My mindset was a result of so many user files being spread across dozens of branches of the Windows file structure. Some very close to the root of the drive, some a few directories deeper. I didn't really understand the benefit of having all my stuff in /home (and am now a full convert. Just thinking about navigating a Windows drive makes my skin crawl now).