Security and privacy rely on a long chain with many weak points. This article (also from The Guardian) discusses this, see link below. It worths reading.

"...if the NSA wants in to your computer, it's in. Period."
"Closed-source software is easier for the NSA to backdoor than open-source software"
"Trust the math. Encryption is your friend."

NSA surveillance: A guide to staying secure
http://www.theguardian.com/world/2013/sep/05/nsa-how-to-remain-secure-surveillance

Free software alone is not enough, unfortunately. For example, remember that a buggy implementation for SSH key generation has been in use for some time until someone noticed it. The good thing is: someone noticed it precisely because source was open, to begin with.

But most people use windows, that's a fact. Everyone knows it is inherently insecure, everybody knows microsoft tells exploits to the NSA months in advance before publishing a patch, and people still close their eyes and keep on using it. However, I don't blame the common windows user: it came with their laptop, after all. It is a de facto monopoly. To use free software only, of course you have to work it hard, but then it gives a heaven of advantages in return.