After having cold/flu symptoms, a bad ear ache came on in my right ear, after about two days the pain spread toy left ear. Both ears felt like they needed to be popped as if on a plane. After three days the pain in both ears stopped but I'm still left with muffled or dull hearing? Is this permanent? What should I do?

There's no way anyone, not even 100 doctors, can know online.
It's common to get ear congestion with a cold or flu, of course, and somewhat common for congestion to linger, if you don't help relieve the swelling, and the drainage down the throat.
That takes a combination of warmth around your ears and neck (scarf and earmuffs or hat pulled way down), lots of liquids (to make the congestion watery instead of like glue), and often a decongestant or anti-histamine (what allergy sufferers take).

Mucous that lingers (lungs, sinuses, ears, anywhere there are membranes, for 2 weeks or more, can allow bacteria in. But you should be able to treat the VIRUS before that happens, with all those suggestions.
Do not make your ears pop.

You should see an ENT.

By the time he gets to see a specialist, at great expense even with insurance, it will be gone, hopefully.
This really is the sort of thing easily treatable by an internist or NP.