I think (?) the difference between this and an atomic reference (of which a Clojure atom is a specific example) is that it is geared towards mutable data structures rather than immutable ones. Although as far as I can tell it's more or less emulating immutable data structures by copying the mutable data structure before modification.

As for the ultimate lack of widespread use of STM in real-world Clojure code, I think in addition to the nice interface provided by atoms, it's also in part because Clojure's STM lacks a couple of combinators that limit its composability, and so a lot of other concurrency approaches make more sense. See the combinators provided by https://github.com/skejserjensen/eclojure and http://www.thattommyhall.com/2013/02/15/stm-clj-vs-haskell/