For some reason unknown to me, when I set my text to 12pt, which is a comfortable printing size, it appears in the document window at what looks like about 6pt to me. I have tried zooming, but that seems to either flip between full screen or half screen or change the font size so it’s comfortable to view but prints at 24pt.
I don’t think you’re missing anything. A 12 point font - especially Times New Roman, for instance - does look rather small in most OS X programs at 100%. You can either scale up the view (using the % pop-up button in the footer bar) to view at 110% or 125%, or use a bigger font and have it changed back to 12-point when printing (using the Compile Draft “Formatting” settings for printing the entire draft, or the settings in File > Page Layout > Settings > Scrivener > Text Options for printing a single document).
Best,
Keith