Faerie has some similarities with
druid, which I just dealt with. Leaving aside the connection both have with magic, both words are often written with an initial capital letter - but not always.
From our vantage point it is easy to imagine that Spenser wrote
faerie because that was the olden times version of
fairy. But actually it seems he invented that spelling as a more archaic looking version of
fairy - which word had been around for a long time before.
Fairy had also been used to mean fairyland: "Þe king o fairy", from a 1330 citation in the OED. It seems like Spenser's spelling didn't catch on all that widely for 400 years or so, but it has been much more widely used in the last 20 years or so. Check out the
ngram chart. As others have suggested, many modern fantasy writers have adopted that spelling to get away from the Tinkerbell connotations of
fairies.
Anyhow, I'm satisfied that
faerie is not a common word. And still less is
faery, which is also classed as common. I'll change them to rare.