KATLPAX
I feel your pain. Having been in this business too many years I have seen this argument over and over.
If you live in an airline hub city, be it in the ME, Europe or the US you will pay more money for a non stop flight out of that Hub city, than a connecting flight through that very same city from one of the spoke cities.
I have not looked at a travel web site, but I am willing to bet a cold one, that if you fly from Muscat or Doha through Dubai to LAX it is far cheaper than boarding that same flight and flying non stop from Dubai. Same could be said, I am sure, if you attempted to fly non stop from Doha to LAX, while a ticket from Dubai to Doha then onward to LAX would be cheaper. It is not the airline, it is the industry. This same point was argued by a prominent UAE businessman in the Gulf news several months ago and he seemed quite angry over Hub pricing, again you have to understand how the airlines price tickets and figure out how to best use it to your advantage. The airlines deem nonstop flight an advantage or a premium to the customer, which they charge you quite happily.
Unfortunately I don't think it will ever change and you will just have to connect thru another Hub to save money.
Good luck