Quite amazing to think MAD was busier than AMS briefly some years ago. Now AMS is 25% busier. Good to see them recovering though!
Just as SCQ83 has explained, MAD-Barajas' main hurdle is not the financial crisis, but the super-efficient high speed rail from Madrid city centre.
Nowadays, the five most important cities of Spain (after Madrid) are linked to Madrid via high speed trains: Barcelona, Sevilla, Valencia, Málaga and Alicante, and this has had an appalling effect on flights between such city pairs. A few examples:
-MAD-BCN: Before the high speed train, there were flights throughout the day every 5-10-15 minutes, many of them in Boeing 757s and Airbus 321s. Now there are just a couple of flights per hour, and many of them do not operate daily basis.
-MAD-ALC: Before the high speed train, there were several flights every day, many of them on AIrbus 321s. Now, there are 5-6 flights per day, at least 2 of them in ATRs.
-MAD-SVQ: Before the high speed train, Iberia used to fly many A300s (!) on this route. I clearly remember flying on a fully booked one and seeing a long waiting list at the gate. Now there are just 3 flights per day on 320s.
The next high speed connection to be introduced will be Madrid-Bilbao, and as a consequence, Spanish AIrlines will lose the last yummy route from MAD to anywhere in continental Spain. Of course there are still interesting markets such as MAD-Canaries and MAD-Balearic islands that are unlikely (joke) to receive the high speed train anytime soon.
Please note that the situation in Barcelona is different. Due to its location, only flights to MAD have been affected, while flights to SVQ, AGP, etc, remain dynamic for Vueling's sake.