Well that depends on how you pronounce FAQ. As soon as words like that get colloquial, they are pronounced as one word instead of as a list of letters (fak vs ef-ay-que).
The New York Times style guide is a handy way to tell: If the Times puts periods between the letters ("A.C.C." for the basketball conference) then it's to be pronounced as individual letters. If the Times puts no periods between the letters ("NATO" for the treaty organization) then it's to be pronounced as a word. That decision is then used to figure out whether there's an "an" in front of it.
The beeb (BBC) works in a similar way. Things that are spelled out are put in all caps ("ACC") and things that are pronounced are put with only a leading capital ("Nato").
Of course, that's just the journalism wonk in me speaking.
Look at the example of the BBC's style guide. If you're using the BBC guide, then things that are all-cap are said using letters. If we wanted to call it the "beebuk" then it'd be "Bbc" (like "Nato").
We just need all high school teachers to find time between teaching basic literacy to teach kids one style guide for these sorts of things.