Ratings are based on averages. An average player playing at about the mid-line of their ability in all phases of the game. Most of us are not equally competent (or incompetent) in all phases. There will be certain courses that are more challenging to a 9 handicapper who has trouble with sloped greens. Another 9 handicapper playing the same course might think it is a cupcake because they are a great putter. Then you take the same two players to another course with flatter greens but narrower fairways and the opinions are reversed because the bad putter is a better driver of the ball.
Finally, most courses are rated by our fellow amateurs (at least in MI). True, there is a manual for establishing ratings but there are bound to be some inconsistencies in the rating process. Much of the work is relatively subjective and the raters often are different from course to course.