Here are some thoughts that occurred to me as to questions to ask yourself:
Font size: Is the map for print or web? Some fonts look better/more legible at particular sizes (letter spacing might become an issue if a font is too big or small), so if the map is for print, make sure you have a font that works at the size it will be printed. If the font is for web, the issue becomes more difficult because the reader can 'zoom in' and out. I guess (don't know for sure) you have to make a decision on font size, based on the map at 100% viewing size, i.e. 1 px on the map = 1 px on the screen.
A big difference between fantasy maps (well the ones we make anyway) and real maps is that real maps are in print and they have a huge number of labels. Smaller fonts are preferred to fit in all the labels. Fantasy maps have relatively few labels so they can be much bigger.
Font Style: We tend to go for 'Fantasy Style' fonts, usually they look handwritten, often with an italic pen or a crow-quill. Apart from obvious cases (say a map drawn by an orc using some heavy handed childlike script) I can't think of any principles to use in deciding which particular style of font to use (assuming it's legible) except for 'what looks right'. We must apply principles subconsciously as to 'what looks right', but apart from the fact that they often need to look a little old (to fit in with the fantasy = old tech, so no proper printing but everything handwritten), I'm not sure what other principles might apply to deciding what 'looks right'.
Font Colour: We tend to almost always use black, and to a lesser extent grey or sepia - presumably for the fantasy = old tech reason?
Hierarchy: I've got map dated 1780 which follows this convention (never noticed it before until I became font mad):
Small villages / towns: Sentence Case, Light, Italic, Small.
Big towns: Sentence Case, Bold (a few in italics), Small.
Cities: ALL CAPS, BOLD (A FEW IN ITALICS), SMALL.
Regions: A L L C A P S, R E G U L A R, L A R G E, E X P A N D E D.
Countries: A L L C A P S, R E G U L A R, EXTRA L A R G E, E X P A N D E D.
What do you guys think? What design choices do you make when deciding what font to use for your map? I'd be really curious to know.