You can end up superheating the water that way and scalding yourself. I also prefer to control the temperature of my water which you cannot do in a microwave.
For superheating to occur, you need very pure water in a smooth container with no imperfections. Tap water in most places cannot be superheated because it contains too many minerals, and most ceramic cups aren't smooth enough to prevent boiling.
If you're making tea, an easy way to prevent superheating is to drop the bag in the water before you heat it. Another way is to put a wooden stirrer in the cup.
There's a mythbuster video here where they show water being superheated: https://www.youtube.com/watch?v=1_OXM4mr_i0, but note that they use distilled water (which nobody drinks) in a Pyrex container (which nobody uses). And they actually use a mug of tap water as a control.
edit: as far as 'nobody' using Pyrex, my preferred container for heating water is a big Pyrex measuring cup.
Eh, I've had it happen many times at home. A coffee mug of water comes out of the microwave with just a hint of bubbles. Add sugar/tea/instant coffee and the whole thing instantly bubbles up and spills.
For a fixed amount of water, you can learn the time and not have to pull out your instant-read thermometer.