Hi, I've always flown Qantas which limits the European destinations. First time I flew Qantas from Sydney to Frankfurt, then Frankfurt to Madrid on Iberia. Both flights booked together through Qantas. This meant that if there was any delay, missed flights etc at Frankfurt, Qantas would guarantee me a place on the next flight. I stayed a couple of nights in Madrid to recover from jetlag, then got the bus to Pamplona, and evening bus to Roncesvalles. There was a taxi waiting at Roncesvalles for pilgrims wanting to go on to SJPP.
Last year, I travelled Qantas/Air France to Paris. I then went on to Lourdes, but you can get the TGV train from Paris to Bayonne, then train from Bayonne to SJPP. A couple of nights recuperating in either Paris or Bayonne would be a good idea before walking.
While cheap airfares are available, as you say they go to odd places like Amsterdam etc. Be careful of these flights because it might cost you more in the long run to get a connection to Spain.