It hurts my eyes when text is #000000 but maybe its because I have a really nice screen with high resolution. I understand it is about what works well but for some, above #000000 is much more comfortable.
I'm the same way, that is why I find it interesting that so many people are complaining that the tips in the article. They definitely help my type of vision a lot. I find #000 very harsh and difficult to read and these softer tons help me.
If I find an article with #000 (or for example... HN comments) I can't sit and read them all at once, I have to go through them in bits and pieces and give me eyes a rest.
Can't you adjust your monitor (usually the "brightness" setting) until it's comfortable for you? Personally, I like keeping the text black and adjusting the background to be darker if I want to reduce contrast.
Why? #000000 is meant to be pitch black, as black as being locked in a room without windows or light. #ffffff is meant to be as light as looking right into the sun itself, blindingly bright. (And my monitor accomplishes quite something like that).
So if I want to be able to play games tweaked for this wide spectrum, and read text, I either just can't, or have to hope websites use grey-on-grey.
That analogy doesn't work because your screen cannot reproduce every color that is perceptible to people.
#000 is as dark as your screen is when the screen is turned off, which is not the darkest color that you can perceive. And if at any point it is uncomfortable to look your screen because it is blindingly bright, then the screen brightness is set too high.
