Bottom line is this: Professionally speaking, my editors don't care what my camera settings are at -- they care about the quality of the image. There is nothing wrong with Auto mode shooting if it gets you a good image, because a good image is the end goal, right?
Now, professionally speaking, I can assure you that if you don't know how to work in M mode you will run into situations where you don't come back with the best image possible. The Auto modes on the cameras are good and getting better but there is no substitute for the human eye. And, sometimes, especially in low or crazy artificial light, the Auto modes in the best cameras can't cut it.
Anyone who claims Auto mode can do everything in every situation has not shot in every situation. It's an ignorant statement. Period. But, anyone who says M mode will always get you a better image is also just as ignorant and probably a little pompous as well.
People on both sides of this argument need to get over themselves. That's my two cents.