I don't think they are scared, it's just easier for them to collect their cut when the payments flow through their systems. It also enables them to do really good customer service and this helps them sell more iDevices. Purchasing, refunds, cancellations are all handled by Apple and are accessible from a single place and that makes for a superb customer experience.
Let's not forget that companies are not charities. When they are charities, they register as such.
