"Working from home" is when you usually work in an office, but for a few days or a short period of time you do your work at home instead:
I'm working from home today, so call me on my cell if anything important comes up.
You can also use the phrase "work from home" to describe someone who always works at home, but works for a company that's somewhere else:
I love my job because they allow me to work from home.
You wouldn't use it, though, for a person who is self-employed. You would say "work at home".