There is a big difference between comfort and stupor. Some software aims to remove the thinking process altogether and guide you down a path gilded with big shiny buttons, to arrive at your destination of Mediocrity, heralded by shoddy defaults. (I don’t know why but software bundled with scanners and cameras comes to mind…).
The coolest tools though are those that remove themselves to the background of your consciousness, so that the job in hand is the primary focus of your attention. Shining examples of these are many text editors such as Geany, Notepad++ and Notepad2, the gloriously minimal writing program PyRoom, the drawing program Inkscape and the web browser Chromium.
I remember an advert by Saab where they made the same point: to be alert you need to be comfortable. Too comfortable and you’ll be asleep. This isn’t such a big problem in front of a computer but pretty darned dangerous at the wheel of a car.