You're paying for someone to write it, supervise it, mark it and provide a flying school for you to do it in.
Bit of a long bow to draw there. By that same logic, the flying school could also charge a student to use the toilet on the grounds that it costs to have the toilets cleaned and plumbing maintained.
To answer your question OP, I was never charged for any of the in house exams. It isn't a particularly good look to charge a student for items such as this when they could achieve the same effect to their bottom line with less of a sour taste in the students mouth by simply charging an extra $5 per hour for the actual aircraft training time.
So whilst it does seem to be a bit of a sour point, I would just look at the big picture as to whether you think you are getting good value training over all, especially when it comes to the quality of your instructors and aircraft for the money you are spending etc.