This is pointed out by Spenser himself in the Gloss to the first eclogue in The Shepherd's Calendar:
"Colin Clout is a name not greatly used, and yet have I seen a poesy of M. Skelton's under that title. But indeed the word Colin is French, and used of the French poet Marot (if he be worthy of the name of a poet) in a certain aeglogue. Under which name this poet secretly shadoweth himself, as sometimes did Virgil under the name of Tityrus, thinking it much fitter than such Latin names, for the great unlikelihood of the language."