DL/UA/AA have much higher fixed costs and overheads (operational, staff, etc) than Emirates, before we even look at anything like fuel on particular routes.

That EK has to pay for "5 hours extra fuel" on such a flight does not mean they are making any less money than DL/UA/AA on the same ticket. They do indeed pay more than the American carriers in fuel on such a ticket - but they have overall lower costs meaning they still come out ahead. I'd wager they're probably making more than the American carriers on such tickets.

I don't have anything comparable showing the American carriers - but this graphic shows you that Emirates' Cost per Available Seat Kilometre (a standard way of comparing airlines' "inherent" costs) is [much] lower than for all legacy European carriers - they're almost into LCC territory:



source

Additionally - airlines that can't offer a direct service will nearly always compete strongly on price. Airlines that offer direct, non-stop services can afford to charge a premium for the convenience. For those that must instead route passengers via a hub, if their pricing is not competitive in comparison with the price of the direct options, the vast majority of passengers would never even consider them - why pay the same/more for a longer journey with a forced stopover/break in the middle when there is a cheaper, direct option available?

If you look at airline pricing, factors such as the markets involved, the routing (indirect vs. direct), the competitiveness of the route, etc, are all far more influential in dictating the price, rather than just the sector lengths/fuel required. Look at the Europe to Australia market vs the USA to Australia market, for instance - much longer distance, but much cheaper prices. And similarly, Australia to Europe is always more expensive than Europe to Australia.

Prices are rarely dictated solely by the distances involved. Many other market forces come into play, too.