There is no way to remove the Paypal button from the shopping cart, or change it's location. It's set by the system and not adjustable. We haven't really heard any complaints of it causing too much confusion, but you could always have text somewhere on your site that explains things if you think its necessary. Perhaps on a Custom Page or in the Welcome Message.
For more on Custom Pages: http://help.zenfolio.com/customer/portal/articles/408187-creating-custom-pages