Even saying "No" costs money. Plus, some customer's tech buddy / kid will do the "upgrade" for them to make the phone "better", the customer will encounter a problem, and then the carrier's support explanation of rooting will make no sense. How often have you seen someone help someone else by changing some settings on their computer?
Often, sure. But that's no excuse for locking people out of their own hardware. Mobile platforms are the future computers for many people, and we simply cannot accept a future where the carriers and manufacturers control all aspects of computing.