Is it just / ?
I kid. But really, besides “its all a file”, if you take away the gui, is the only difference the syntax ? How libraries interact? How disks are mounted ?
If we stripped all ms’s junk out and made windows open source, would we still prefer linux?
When you get to a very basic level, is one of them more efficiently coded?
The licensing: Free and open source vs. paid, proprietary, and closed source. That really is the core difference, the licensing, and all the differences that come as consequences of that difference.
What separates the Linux kernel from the (Free)BSD kernels is copyleft/reciprocal licensing vs. permissive licensing.