I hardly know where to start.
First, the line for just getting a reservation on the AVE often takes just as long as the trip itself. It has assigned seats just like a plane, you can't just walk on and sit wherever you want.
Absence of security screening? Whoever wrote the article obviously never took the train, and never asked anyone who has. There is security screening at both Madrid's Atocha station and Barcelona's Sants station. Does no one remember the 200 dead after the Atocha bombing?
The puente is a highly vital to passengers departing from Barcelona, connecting through Madrid to destinations not served (or unde-served) by direct flights from Barcelona. The same goes for passengers heading for Barcelona who can't get direct flights and have to first fly to Madrid. For example, the evening flight from Barcelona to back to Düsseldorf does not run daily, and is often full when it does. I have often had to fly from Barcelona to Madrid to connect to a flight home in the evening.
While Madrid's Barajas airport is indeed far from town, Barcelona's airport is not too bad a ride, and I usually am at my destination in the middle of town by taxi in half an hour or less after landing.
Now, for travel only between the two cities, I would indeed prefer the train, even if it's more expensive (as with flights, fares vary widely). You can get decent food, and the landscape is quite a scene. Take the nonstop if you can, since the half hour you save can be spent doing something more fun. But both trains arrive at crowded stations, and finding public transportation, especially in Madrid, can be a long wait and cumbersome.