This site, like some name books I know, explains CHUCK as a pet form of CHARLES. Now Hanks & Hodges come up with something different:
It derives from the English term of endearment, itself probably from Middle English chukken to cluck (of imitative origin). It is now often used as a pet form of Charles.
(Hanks & Hodges, Oxford Dictionary of First Names, 1992)
What shall we think of this?