Using the command-line doesn't make you a better programmer and doesn't help you understand your computer better. What makes you a better programmer is the code you write, and it frankly doesn't matter if you write it using an IDE, command-line tools, or even a washing machine. Use the tools that you feel most productive with yourself and never mind what anyone else tells you you should be using.

If you want to be a better programmer then the OS you use is probably the least important thing. Write something, release it and be humbled (and releasing stuff publicly can be an incredibly humbling experience - just watch your carefully crafted code crash and burn horribly on a multitude of different systems owing to edge cases you never even thought of), learn from the experience and your mistakes, repeat, and you will get there.

If you consider all the Free Software stuff, Linux will be obviously better, but that's an option, and it doesn't have anything to do with the programming itself, so decide the one you like more. I use Linux right now and don't have problems, but have Windows too in another partition and if I make a program for Windows I will use it of course. However, I always try to make things multiplatform, so it''s just compiling in the diferent systems. In that case I program in Linux, just because I like it more, there's no other reason.