From William Donaldson, The Jacobite Song: Political Myth and National Identity (Aberdeen University Press, 1988), p. 104:

By no means all of Hogg's Jacobite songs found their way into the Relics. One of the most famous, 'Bonnie Prince Charlie', was first printed in The Border Garland, a pamphlet of nine songs issued in 1819. It reappeared in the edition of the Shepherd's Songs in 1831 with the following disparaging note:

Is it not singular how this song should have been so popular? There can be no dispute that it is one of my worst. The air was...given me by my friend the late Mr Neil Gow, and to it I dashed down the words at random.