I bet Audyssey got the sub level correct. You should NEVER hear a sub. It should be seamless and no one should ever be aware of its presence. I find subs are turned up too high very frequently, in fact more often than not.
Part of this is compensation for inadequate speakers. I do not subscribe to the view that bookshelves and subs gives a comparable experience to capable speakers and a sub or subs. Better is full range speakers that require no subs, but this is seldom practical for most. Most of the program that is perceived as bass is actually well above sub range. Good bookshelves will only deliver this in the smallest of rooms. This is the number one reason why people turn up the subs.
The other reason is that "I paid good money for these subs and I jolly well want to hear them!"