I kind of like them and they meet the needs of most people in a clean and tidy fashion.
Sure there are bad ones, but there are just as many bad setups outside of entertainment centers. In fact, probably more bad setups outside of them, since people are forced by an entertainment center to at least put a their TV in a moderately sensible location (eg, not over the fireplace) and speakers in moderately sensible locations (eg, not piled on top of the TV table or on the floor). So they almost force a basic modicum of a decent setup by forcing some basic geometry that people left to their own devices get wrong.
Give the average person a blank slate, and they really really really get it wrong, so very very wrong, so very very often. The entertainment center is like training wheels for such people. It also greatly increases the ever important spousal acceptance factor when starting out. (Look honey I'm not crazy. The builder even put spaces for all this stuff into our home for a neat look!)
On there other hand, the entertainment centers don't tend to be a problem for people wanting better quality, if they are smart about it:
As long as one understands acoustics, SBIR, diffraction, baffles, viewing angles, wire management, bass management, ventilation, and so on, and uses that knowledge in how one approaches the entertainment center, the centers are quite workable and don't have to limit one.
Not enough space for a TV? Pop a electric screen in front. No budget for wire management and installation services? Just use the wire management in the center, itself. Etc.
Now, I know that sounds like a lot of engineering in order to get it right but let's face it, you would have to know lots of science of sound and vision to get it right with or without an entertainment center, so there's not much difference there.