Air Swift (http://air-swift.com) has at least daily flights to Manila, Caticlan (for Boracay), Cebu and Clark. One-way fares range from P4500 to P7000, depending on the season. All flights are into Lio Airport, 7km north of town (P200 by tricycle). Air Swift and the airport are both owned by El Nido Resorts, and guests of that company's resorts have priority on the flights, although there is usually plenty of room for outsiders.
Many people heading to El Nido take a cheaper flight to Puerto Princesa, then drive north five hours by van. The newly opened airport in San Vicente will potentially cut that van trip in half, but at the time of writing there were no commercial flights. Sandoval Airport in Taytay, just an hour from El Nido, is in the process of upgrading in the hope of landing commercial flights.