1. Control. Absolute control over a huge chunk of worldwide B2B and B2C transactions is extremely valuable per se, in political and commercial terms. It's power that can be leveraged in a number of ways which are not necessarily reflected in the balance sheet. Bezos just bought the most influential newspaper in US political circles; this guy knows a thing or two about setting the agenda.
2. There is corporate profit and personal profit. Amazon employees are themselves turning quite a bit of personal profit. Does that make Amazon a No-Profit ? That's debatable. As someone else mentioned, pure profit is easy to tax, while "operating expenses" and share dealing can be shuffled around.
3. Industrialism. Many XIX-century industrialists saw their companies as agents of change as well as sources of profits. Amazon is pushing the envelop in commercial infrastructure (fully-automated warehouses, software-enhanced packaging, customer-seller variable relationships, etc etc) as well as creating whole new markets (AWS). As long as they don't start bleeding money, they're running a self-sustained engine of change, which is an achievement in itself.