It tends to encourage you to buy at the outset a ticket for the cabin you want to travel in, rather than playing games with cheap after-purchase methods of getting up into that cabin. The application of a change fee is not the only tool used to this end: restricting the number of AUPs you're allowed to buy is another one; delaying the appearance of POUGs is another.

There are some airlines that don't charge a change fee for an upgrade to a higher cabin on the same flight, but AIUI they are in a minority.