Madden and Call of Duty don't use football equipment and guns, though, and that's the difference in perception.
I'll grant you that what you just said is a big part of this mindset, but versapak hit the nail on the head. The guitar hero guitar has five buttons. These 5 buttons create song after song and simply because it's shaped like a real guitar people assume you are wasting your time "learning the toy" when you can just as easily learn the real thing.
I'm convinced that a lot of folks are so ignorant to instruments that they really think you could learn guitar from Guitar Hero.
Plus, Madden may not be using football equipment... but plenty of games have add on peripherals without this reaction. If my friend is really good at Gran Turismo with his wheel, should I be making fun of him because he's not really racing around a mountain pass in a $200k car? Or if you are really good at Ace Combat with the flight controls, are you wasting your time by not flying fighter jets?
It's just a pet peeve of mine. I actually find it funny because it's just so strange that this one particular game has created this feeling where a lot of other peripheral games have not. Then again, not many games with specific controls have gotten as mainstream as this, so I guess it's to be expected.