Magento is really two different things -- the thing most people associate with the brand is the shopping cart, which is actually free and open source. Magento also offers a suite of ecommerce services, including various kinds of tracking, cart management and customisation, and more. None of those services are free, and none of them were before eBay bought Magento -- like many other open source software concerns, they offer an excellent free piece of software, and make their money on customisation and enhanced services.
Frank