The term derives from Cabala, which refered to a particular kind of Scriptural mysticism, and originally meant either an occult doctrine or a secret, but gradually developed its meaning of intrigue and conspiracy. Its usage still carries strong connotations of shadowy corners and occult influence; a cabal is more evil and selective than, say, a faction, which is simply selfish.
During the rise of Usenet, the term gained great coinage as a semi-ironic description of the efforts of people to maintain some order over the chaotic, anarchic Usenet community; see backbone cabal, There is no Cabal.
See also zealot, thug?, and assassin for other negative words which came from words describing religious extremism or religious sects.