DISCLAIMER: I hate air travel, but do it most weeks.
I have worked in and around the safety critical software industry for over 20 years. The level of testing and certification that the flight control software for a commercial aircraft is subjected to far exceeds any other industry I'm familiar with. (I'm willing to be educated on nuclear power control software however.)
The actual problem on the Qantas jet was a latent defect that was exposed by a software upgrade to another system. So the bug was there for a long time and I'm sure there are still others waiting to be found. But this doesn't stop me getting on a jet at least twice a week.
As a software professional and nervous flyer, do problems with the aircraft software scare me? No not really. What scares me is the airline outsourcing maintenance to the lowest bidder in China, the pilots not getting enough break time, the idiotic military pilot who ignores airspace protocol, and the lack of english language skills in air traffic controllers and cockpit crew across the region where I fly (English is the international standard for Air Traffic Control).
A good friend is a senior training captain on A330's, and in all the stories he tells software is barely mentioned. What get's priority in the war-stories is the human factors and general equipment issues - dead nav aids, dodgy radios, stupid military pilots. One software story was an Airbus A320 losing 2 1/2 out of 3 screens immediately after takeoff from the old Hong Kong airport. The instructions on how to clear the alarm condition and perform a reset were on the "dead" bottom half of one of the screens.
A great example of software doing it's job is the TCAS system - Traffic Collision Avoidance System (http://en.wikipedia.org/wiki/Traffic_collision_avoidance_system). To quote my friend "If it had lips, he'd kiss it". It's saved his life, and the lives of 100's of passengers, at least twice. Both times through basic human error on the part of the pilot of the other aircraft.
One final thought - on average about 1000 people die in commercial aviation incidents each year world wide (source: aviation-safety.net) . In the USA, over 30,000 people die in vehicle accidents every year.