I´m currently flying A-320, I´ve also flown B 737(300 and 800), and MD88. It´s true that at the beginning the new airbus received a lot of heat from pilots. After all they were trying to reinvent cockpits UI from 0. This led to a series of design accidents (due to initial design mistakes ) like the one on the article.
The initial idea it´s not bad: reducing weight (removing all mechanical and hydraulic controls), inventing the glass cockpit, simplified system management, etc..
It took over a decade to polish the cockpit (and the whole airplane, that had tons of electronics related failures all around) to it´s actual safe and workable state. Those issues, plus the idea that pilots had to readjust your whole idea of a cockpit, were the ones that created that opposition. The opossition it's almost gone now, although in general we pilots still prefer Boeing aircraft (at least in Europe). Airbus airplanes fly very nicely and are great too.
But now that we are used to the new IU, the concept problems are still there.
Main diference between flying normal fly controls and a moving auto-throttle and airbus fly-by-wire:
-Airbus throttle levers don´t move while the auto-thrust is changing the power setting. All the other airplanes as far as I know do it.
-Airbus side-sticks don´t move when the autopilot or the other pilot is giving an input. Also as somebody explained above, the inputs are added, you can end with a double (or zero input), if you forget to push the priority button (in stress situations like last second corrections to land it´s easy to forget it).
Why this is a mistake? because when flying a modern airliner you have an excess of information to process, all at once. A moving auto-throttle let´s you know what the engines are doing through your hands, without having to look at a tiny indicator at the instruments. Also it let´s you override the auto-throttle briefly because you need more power or less power at a given moment, without having to disconnect it. With airbus auto-thrust either the airplane or the pilot has the control, and you have to manually takeover. This may be dangerous at an approach that it´s already hard enough with cross winds or heavy rain.
The same apply to the side-stick. Normal autopilots move the fly controls at the cockpit while actuating them. This let´s you know what the autopilot it´s doing. And of course when a pilot it´s flying manually, the other pilot knows exactly what he is doing ALL THE TIME. He can slightly correct a maneuver without having to take over the controls from zero.
Airbus has wiped a layer of fundamental information available to the pilots, increasing the information overoosd through the vision. It´s the equivalent of driving a race car with a playstation control. Most of the time this information it´s not used(like in cruise), but you really, REALLY need it when things become hairy close to the ground. In fact I routinely disconnect the auto-thrust to land, with the Boeing and MD88 I kept it engaged.
Airbus knows this, but it´s too late to change 20 years of airplane development. They´ll need to change too many things (systems, procedures, certification, instruction), also right now it´s easy to change from flying let´s say a A320 to a A 330, due to having very similar cockpits and systems (that´s a great idea). The conversion course it´s short and relatively cheap. Changing the controls would make this fleet changes much more expensive and time consuming to Airlines.
Edit: overall small changes to improve clarity.