Exactly. IO is nearly the worst first Monad to learn, because none of the internals are visible, making it look far too magic. (Only something like Cont would be worse.) The best choice would be something like Writer or State, where you can see exactly what the abstraction hides, why you'd want it, and how it would look if done via explicit state-passing.
Yes, something like WriterT Error is a great "default state" for your functions: they can produce a correct answer, an error, and some logging information. Programmers love punting things like error handling to higher levels of their program; why not do that with logs, too? (And, given a correct implementation of Writer, if you ignore the log messages, they aren't computed. Try that with Java!)
