Harmon said:
How do you harm something in M&M that has more protection then you have ability to do damage? (Ya, I know the obvious- do more damage

)
Ok everyone else has covered the direct answers already. Within the rules, there are plenty of ways to overcome the over-protected villain.
So, i will add only a more indirect train of thought... maybe you ought to change your gaol. What if beating him "right now" is not possible? Think of how many different times in stories or comics that was the case... where the first or even second encounters were "impossible".
Maybe there is more to this particular scenariop/story than "bang him 'til he drops"?
So, after knocking your head against the brick wall, think of other ways to "beat" the villain.
First, what is he there for? If its to capture someone or something, can you stop him from getting it? Can you snag it and run (are you faster than the bad guy or able to fly/swim etc when he cannot?) Can you distract him or slow him down enough that he cannot wait? hecvk, in dire extremis, can you break the thing he is going for?
Second, is there anything local that you can use against him, or draw him towards? is he ronotic? if so how about EMP from blown transformers, or shocks from electrical powerlines? is he electrical? if so how about metal ground wires or water? Basically, what special weaknesses does he have that you can possibly try and exploit?
Third, if all that draws a blank, what can you learn from him that you can use later? Can you scan his ff for energy signatures and go back to the lab and research? Can you get a sample of his uber-armor's material for stufy? What can you do to setup the olde fahsioned "back to lab to develop counter so NEXT TIME we have a chance~" scenario?
Fourth, if all else fails, can you get out of the way? Specifically, can you get innocents out of the way? get the civies out of harms way while the most distracting guys simply try and slow him down. You are not trying to win right now, cuz you got nothing, but you are trying to, quite heroically i might add, cut loses and save people.