It's mostly because in an emergency situation where you're panicking people sometimes goof it up and hit the accelerator when they need to break and get into an accident.
I found out that, from a legal standpoint, if you get into an accident and they find out you drive with both feet instead of one, you can be charged with careless driving or dangerous driving.
manual with both feet, automatic with one.. it is considered bad because if you're used to driving manual, your second leg should be used only for clutch and you have to press the clutch completely for changing gears.. and when you shift to automatic, if you use the same leg you were using for clutch, for brakes, you might press the brakes really hard and the car would almost come to a stand still and someone will bang you from behind