Does the use of a hyphen really prevent confusion in this case?
can any words use with hyphen ?
These seem to be two different concepts to me. Cooperate is to work together in any circumstance, and co-operate is when two or more people operate a specific machinery together.
Ex.) The girl and boy cooperated to produce a lovely sand castle.
Ex.) The machine was so complicated to work on that Bill and Mary co-operated it.
I agree. They're two separate words. The hyphen causes you to focus on the word "operate".