Two things I really like about Scrivener in this regard:
The sense of freedom I have to format my writing space to suit my writing in the clear knowledge that this is can be done entirely independently of the format of my compiled typescript.
Scrivener gives me two built-in regimes for writing that can have their own settings—the Editor pane and Full Screen. I use these differently, and I find it utterly natural to use different font scales for the two spaces.
I do most of my work on a 12" laptop screen, and I like sizeable, easy to see text, because it “frees me from the screen”, i.e. reduces eye fatigue and unglues your face from the monitor, restoring head and body mobility while you work.
My currently preferred typeface is Courier (yes, back to Courier. feels like coming home). I have is set to 18 pts by default, but I use the “scale %” pop-ups to scale adjust this. In the Editor, I use 100% and 125%, depending on what I am doing. In Full Screen, I am always just gang-out writing (or reading–though I often pull things up into Tofu for real reading to eliminate the annoyance of vertical scroll), so I keep full screen set to sumptuous 150%.
May seem big to you, but you should try it. I think people don’t realize how much time they spend looking at tiny type on their computer and don’t realize how much focussing on tiny type on a monitor over a period of time immobilizes you and taxes your eyes.
Sometimes you absolutely need to see more of your text in a window, but often not. Scrivener works pretty ideally for me in navigating between these two opposite-going needs.
UPDATE (Aug 2010): While the principles remain, my practice has changed. I have decided it gives me more flexibility to keep the default text set to 12 pt Courier and do all the scaling with magnification. In this case, 175% in the Editor and 200% for Full Screen. The net result on screen is the same, BUT I there is a boon to doing it this way. The chief advantage of going this route is that I can make quick printouts with Scriv’s Print function (as opposed to Compile) of a document or documents (via Edit Scrivenings) and these then come out in a clean, “manuscriptish” 12pt Courier without any fuss. (I know the Print function can be set via Page Setup to use the current compile settings, but for my quick-and-dirty drafty printouts it is for some reason better for them not to have that finished look.)
So, the bottom line now is: a) set Editor font size according to desired size of quick-and-dirty Print printouts, then b) use magnification in Editor and Full Screen to achieve sumptuous, kick-back font size on screen. For me, that is i) 12pt Courier with ii) 175% and 200% mag, respectively.