I'm having trouble finding a flight. I've tried Cebu Pacific, SEAIR, Asian Spirit, Phillippines Airlines, and Air Philippines, but none of their websites indicate there is a flight from Puerto Princessa to El Nido. Is this accurate? If so, can anyone suggest a quick and painless way to get there?

Check SEAir again.
Sat and Tue according to their webpage. The flight Pto Princesa-Busuanga say 'via ENI'.
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Hi, SEAir should be ok, as #2 mentions.
If they are full, or you need to fly on a different day, you can also try Island Transvoyager. Give them a call at +63 2 8515667 or try emailing info@islandtransvoyager.com.
I think guests at El Nido resorts get priority on ITI flights, but you can check to see if they have seats available. They have a map to the hangar on their web site at http://www.islandtransvoyager.com/ - but you'll have to contact them for info on fares. I've flown ITI but that was over a year ago so I'm not sure what their current fares are.
Hope this helps!