The derivation of the Hanlon eponym is not definitely known, but a very similar remark ("You have attributed conditions to villainy that simply result from stupidity.") appears in "Logic of Empire", a classic 1941 SF story by Robert A. Heinlein, who calls it the `devil theory' of sociology. Heinlein's popularity in the hacker culture makes plausible the supposition that `Hanlon' is derived from `Heinlein' by phonetic corruption. A similar epigram has been attributed to William James, but Heinlein more probably got the idea from Alfred Korzybski and other practitioners of GeneralSemantics.
According to http://www.mindprod.com/unmain.html ,
"Never ascribe to malice, that which can be explained by incompetence" is a quote from Napoleon.
It's also been attributed to Machievelli. Hanlon as a corruption of Heinlein sounds more plausible, but this stuff is basic folk wisdom that's no doubt been repeatedly thought up and independently expressed over centuries.