It's a matter of marketing. Everyone knows it's based on Ubuntu, so they feel cheated when they're asked to pay for a free OS.
A marketing solution is to sell it as:
* base system $0 - VM with free download, no whines about "cheating". And the base VM gets you an Ubuntu image which boots to a shell prompt.
* Elementary additions: $$. The base system plus our less-filling, weight-loss inducing proprietary magic!
People are happy to pay money for linux application. Not many people, and for not a lot of money. But people do pay.
Having happy paying customers is a lot better than calling your potential customer base "cheaters". That's just stupid .